More info about the MCA app required

Applications, development tools, FPGA, C, WEB
pavel
Posts: 616
Joined: Sat May 23, 2015 5:22 pm

Re: More info about the MCA app required

Post by pavel » Sun May 17, 2020 9:35 am

Thank you for sharing all the screenshots. I'm glad that you've found a configuration that works well for you.

I'm also curious to understand why the pulse duration is much longer than 320-350 ns that you originally mentioned.

Since the pulses have undershoots because of the AC coupling and the baseline is moving quite significantly, I'd suggest trying the automatic baseline mode to improve the resolution. In automatic mode, the baseline level is defined as the minimum value just before the rising edge of the analyzed pulse.

I'd also suggest trying different values of the decimation factor. Maybe setting it to 8 or 16 could improve the resolution.
There is also no energy calibration field nor temperature adjustment...
It's by design. The application only does the data acquisition. It doesn't have any data analysis functionality.

The data analysis should be done by specialized tools like InterSpec or analysis scripts written in Julia, Matlab, Python, etc.
Bins are limited to either 1024 or 16656 samples. -- more typical is 2048 and 4096bins
The histogram in the FPGA configuration has a fixed number of 16384 bins. The re-binning to 1024 bins is done by the javascript code of the web interface.

There is nothing typical about 2048 and 4096 bins. Nowadays, many commercially available multi-channel analyzers have 8k or 16k bins:

https://www.amptek.com/products/multich ... l-analyzer
https://www.ortec-online.com/products/e ... lyzers-mca
http://www.caen-group.com/csite/CaenFly ... parent=228

CJWestshore33
Posts: 29
Joined: Sun Dec 07, 2014 5:41 am

Re: More info about the MCA app required

Post by CJWestshore33 » Sun May 17, 2020 4:18 pm

pavel wrote:
Sun May 17, 2020 9:35 am
Thank you for sharing all the screenshots. I'm glad that you've found a configuration that works well for you.

I'm also curious to understand why the pulse duration is much longer than 320-350 ns that you originally mentioned.

Since the pulses have undershoots because of the AC coupling and the baseline is moving quite significantly, I'd suggest trying the automatic baseline mode to improve the resolution. In automatic mode, the baseline level is defined as the minimum value just before the rising edge of the analyzed pulse.

I'd also suggest trying different values of the decimation factor. Maybe setting it to 8 or 16 could improve the resolution.
There is also no energy calibration field nor temperature adjustment...
It's by design. The application only does the data acquisition. It doesn't have any data analysis functionality.

The data analysis should be done by specialized tools like InterSpec or analysis scripts written in Julia, Matlab, Python, etc.
Bins are limited to either 1024 or 16656 samples. -- more typical is 2048 and 4096bins
The histogram in the FPGA configuration has a fixed number of 16384 bins. The re-binning to 1024 bins is done by the javascript code of the web interface.

There is nothing typical about 2048 and 4096 bins. Nowadays, many commercially available multi-channel analyzers have 8k or 16k bins:

https://www.amptek.com/products/multich ... l-analyzer
https://www.ortec-online.com/products/e ... lyzers-mca
http://www.caen-group.com/csite/CaenFly ... parent=228
Actually the MCA app is actually set to Auto baseline, otherwise the data that would show would distort or disappear all together. In the settings the sample rate is also set to the fastest available. 35nS.
Going down in sampling speed lead to clipping of my spectrum in various energies. Giant gaps.

Regarding binning. It is still pretty typical to have multi bin rates. 1024, 2048, 4096... etc....
16K is used more for HPGe and some very fast high res. scintillation mediums such as LaBr3:Ce.
Digital PMT bases are still running only up to 2048 by AMPTEK, this rate is selectable in software.
The number of channels can be changed in most modern gamma spectroscopy system by changing a software or hardware setting. Common values include 512, 1024, 2048, 4096, 8192, or 16384 channels. The choice of number of channels depends on the resolution of the system and the energy range being studied."

In this particular application the 16K bin rate ends up being severely aliased anyways so it cannot be used when exported to Interspec. I tried numerous way to get it to work. NaI/Tl is not high enough resolution to warrant 16K samples.

pavel
Posts: 616
Joined: Sat May 23, 2015 5:22 pm

Re: More info about the MCA app required

Post by pavel » Sun May 17, 2020 6:18 pm

Unrelated to the MCPHA application. I've just realized that the Red Pitaya board on the photos in your previous messages doesn't have active cooling. The heat sink supplied with the Red Pitaya boards doesn't cool them effectively. Here is a link to an article with a graph showing the temperature of the ZYNQ chip:
https://rroeng.blogspot.com/2014/03/kee ... -cool.html

Without active cooling, the temperature of the ZYNQ chip dangerously approaches the maximum operating temperature for the commercial grade ZYNQ chips used on the Red Pitaya boards. I've heard of a few cases where the passively cooled Red Pitaya boards have stopped working after a few days of operation.

A 5V 30x30mm fan can be easily attached to the heatsink with a couple of screws and it would keep the temperature of the ZYNQ chip around 40 degrees.
In the settings the sample rate is also set to the fastest available. 35nS.
Going down in sampling speed lead to clipping of my spectrum in various energies. Giant gaps.
Thank you for checking the other decimation rates. If 64 ns (decimation rate 8) doesn't work, it's probably because the rise time of the pulse is faster than I thought looking at the screenshots and it's too fast for higher decimation rates.
The number of channels can be changed in most modern gamma spectroscopy system by changing a software or hardware setting. Common values include 512, 1024, 2048, 4096, 8192, or 16384 channels.
OK. I see now what you mean. Normally, I do rebinning from 16k to a lower number of bins in my analysis scripts. However, I agree that it might be useful to have the possibility of changing the number of bins in the data acquisition code. I'll see how it could be implemented in my code.

I've just checked how the rebinning is done in the javascript code. Looks like the main part is on lines 543-558 in app.js:
https://github.com/sefffal/redpitaya-mu ... #L543-L558

There is also some code that depends on bincount on lines 624-626 in app.js:
https://github.com/sefffal/redpitaya-mu ... #L624-L626

I think it should be relatively easy to add a few other bincount values (2048, 4096, 8192) to the javascript code.

CJWestshore33
Posts: 29
Joined: Sun Dec 07, 2014 5:41 am

Re: More info about the MCA app required

Post by CJWestshore33 » Mon May 18, 2020 8:25 am

Good point about the RedPitaya.. I have a case for the board but I am unsure how effective it
will be in keeping the board/FPGA cool. hmm, this has me thinking... As you've stated the FPGA gets quite hot and I definitely noticed this...almost warrants a larger heatsink--copper perhaps...like the ones used on graphics cards? hmm... :geek:

The pulses from the NaI/Tl detector are 8-10x longer than the shortest pulse width measureable
in the program... 280-350nS so I was surprised to see clipping even at below 200nS even at 64nS. Maybe this is due to dynamic frequency scaling taking effect on the FPGA as it heats up?

I am still wondering what might be the cause of a blank screen when turning off the log.view in the MCA histogram window. Is that an incompatibility with the recent OS update? I tried playing with this again and the histogram showed albeit very briefly before totally disappearing. Linear or Sqrt.

I'd like to figure out the sampling issue... I am going to retry my experiment and also give your MCA app a try with the PHA program to see if I can obtain a different result.
Hopefully I can side load that on Red Pitaya app page by SSH'ing via putty. You suggested I might be successful in doing so.

pavel
Posts: 616
Joined: Sat May 23, 2015 5:22 pm

Re: More info about the MCA app required

Post by pavel » Mon May 18, 2020 8:46 am

Hopefully I can side load that on Red Pitaya app page by SSH'ing via putty.
If you have an SD card with an image downloaded from this page, then the easiest way to install the MCPHA application is to use the application marketplace:
  • open a web browser and go to the IP address of your Red Pitaya board
  • click on the application marketplace icon
  • scroll down to MCPHA and click install

CJWestshore33
Posts: 29
Joined: Sun Dec 07, 2014 5:41 am

Re: More info about the MCA app required

Post by CJWestshore33 » Thu May 21, 2020 4:00 am

hmm, I tried to find your app via the application marketplace... there seems to be missing applications as I only see a broken page. Did this page get taken down? :?



I am going to have another go at trying to find your MCA app later as I ran out of time trying to find it.

:?

pavel
Posts: 616
Joined: Sat May 23, 2015 5:22 pm

Re: More info about the MCA app required

Post by pavel » Thu May 21, 2020 11:39 am

hmm, I tried to find your app via the application marketplace... there seems to be missing applications as I only see a broken page. Did this page get taken down?
I'd suggest to check if your Red Pitaya board can access the Internet and the Red Pitaya bazaar web page. The simplest test I can think of is to run the following command from the Red Pitaya command line:

Code: Select all

curl -s http://bazaar.redpitaya.com/ | grep MCPHA
If the connection is OK, then the command should return the following line:

Code: Select all

MCPHA (1.0-20190527)
I've just downloaded and installed the latest stable SD card image (STEMlab_125-xx_OS_0.98-696_stable.img) from this web page, then installed the MCPHA application via the application marketplace without any problem. I've just clicked on the 'Application marketplace' icon and then on the 'Install' button under the 'MCPHA' icon.

Here is a screenshot of the board's web interface showing the already installed MCPHA application and the 'Application marketplace' icon:
web_interface.png
and here is a screenshot showing the MCPHA application as seen from the application marketplace application:
bazaar.png
When the application is already installed, the 'Install' button is replaced by the 'Run' and 'Uninstall' buttons.
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pavel
Posts: 616
Joined: Sat May 23, 2015 5:22 pm

Re: More info about the MCA app required

Post by pavel » Thu May 21, 2020 2:31 pm

Since I now have an SD card with the Red Pitaya ecosystem, I've tried to install and modify the web interface by Will Thompson. I think that I've managed to add more bincount values (2048, 4096, 8192) without modifying the code too much. Here is a link to the corresponding pull request:
https://github.com/sefffal/redpitaya-mu ... ser/pull/6

I cannot reproduce your problem with the linear scale of the y axis. Switching from and to the logarithmic scale works very smoothly in Firefox.

I've noticed that in the web interface it's possible to set the 'Wait Time' parameter to 0. I don't think this is a good idea. I'd suggest keeping this parameter at its default value.

CJWestshore33
Posts: 29
Joined: Sun Dec 07, 2014 5:41 am

Re: More info about the MCA app required

Post by CJWestshore33 » Sun May 24, 2020 5:07 am

pavel wrote:
Thu May 21, 2020 11:39 am
hmm, I tried to find your app via the application marketplace... there seems to be missing applications as I only see a broken page. Did this page get taken down?
I'd suggest to check if your Red Pitaya board can access the Internet and the Red Pitaya bazaar web page. The simplest test I can think of is to run the following command from the Red Pitaya command line:

Code: Select all

curl -s http://bazaar.redpitaya.com/ | grep MCPHA
If the connection is OK, then the command should return the following line:

Code: Select all

MCPHA (1.0-20190527)
I've just downloaded and installed the latest stable SD card image (STEMlab_125-xx_OS_0.98-696_stable.img) from this web page, then installed the MCPHA application via the application marketplace without any problem. I've just clicked on the 'Application marketplace' icon and then on the 'Install' button under the 'MCPHA' icon.

Here is a screenshot of the board's web interface showing the already installed MCPHA application and the 'Application marketplace' icon:
web_interface.png

and here is a screenshot showing the MCPHA application as seen from the application marketplace application:
bazaar.png

When the application is already installed, the 'Install' button is replaced by the 'Run' and 'Uninstall' buttons.
So I had another go at getting the MCPHA app today via the application marketplace. I am unable to connect to it. I kept getting:

ERROR 404
Not found


Protocol error while connecting to Bazaar server.

Consult Nginx error log for details.

OK, return to my Red Pitaya.
b]Protocol error while connecting to Bazaar server.

Consult Nginx error log for details.

OK, return to my Red Pitaya.
[/b]
However I can see the resource by SSH that you posted about available in the bazaar (github) and will randomly (every 2 or so times) throw an error back saying the resource is unavailable.
When I run wireshark I can see my MAC address of my red pitaya is being rejected from the main server. So, it is essentially the same Nginix error from 2016.

pavel
Posts: 616
Joined: Sat May 23, 2015 5:22 pm

Re: More info about the MCA app required

Post by pavel » Sun May 24, 2020 10:50 am

Have you tried the latest stable SD card image (STEMlab_125-xx_OS_0.98-696_stable from this web page) that worked for me?
However I can see the resource by SSH that you posted about available in the bazaar (github) and will randomly (every 2 or so times) throw an error back saying the resource is unavailable.
When I run wireshark I can see my MAC address of my red pitaya is being rejected from the main server. So, it is essentially the same Nginix error from 2016.
I'm afraid that I don't understand most of this part. I don't know what resource and what error from 2016 you're referring to.

If you're really sure that the bazaar's web server is the source of the problem, then I can only suggest sending a detailed description of the problem to Red Pitaya support (support@redpitaya.com).

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