Converting PDZs to CSVs

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Arlen Heginbotham

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Apr 16, 2019, 12:40:54 AM4/16/19
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Greetings all,


I was wondering if anyone could guide me on a way to batch convert a large number of Bruker .pdz files into .csv files?


Thanks and sorry if this has been addressed before!


Arlen Heginbotham
Conservator
Decorative Arts and Sculpture
The J. Paul Getty Museum
1200 Getty Center Drive, Suite 1000
Los Angeles, CA 90049

Lee Drake

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Apr 16, 2019, 2:13:50 AM4/16/19
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Hi Arlen,

In S1PXRF, go to Setup -> Group Conversion

1. Browse to the directory with the PDZ files and select one (it will grab the whole folder)
2. Check "Output CSV"
3. Process!

That can process hundreds of thousands of spectra at a time. I strongly, strongly, strongly, strongly recommend anyone who has PDZ files do this. PDZ files are a proprietary format that is dependent on software that is no longer under development (S1PXRF). If a future windows update breaks compatibility with that software, then those PDZ files are end of life. CSV files, on the other hand, are open source, as future-proof as is possible, and can be manipulated in Excel if needed. I cannot recommend strongly enough how important it is to have a copy of all of your data in an open-source format.

Note that you can also export as a txt file - but this has less metadata than the csv files. I think csv files are hands down the best way to archive XRF spectral data. If you don't have a Bruker, please inquire about how to archive your data to a CSV or open-source format as well. It is absolutely crucial to preserve the data.

Thanks,

- Lee

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Arlen Heginbotham

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Apr 16, 2019, 1:38:26 PM4/16/19
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Thank you, Lee!


Arlen Heginbotham
Conservator
Decorative Arts and Sculpture
The J. Paul Getty Museum
1200 Getty Center Drive, Suite 1000
Los Angeles, CA 90049
From: px...@googlegroups.com <px...@googlegroups.com> on behalf of Lee Drake <b.lee...@gmail.com>
Sent: Monday, April 15, 2019 11:10:51 PM
To: px...@googlegroups.com
Subject: Re: [pxrf] Converting PDZs to CSVs
 

Bruce Kaiser

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Apr 17, 2019, 8:21:21 AM4/17/19
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ARLEN
If you do not have S1PXRF
Go to Bruker web site downloads Tracer 5i
Down load S1PXRF
AND INSTALL
THEN
OPEN ONE OF PDZ FILES IN YOUR FOLDER IN S1PXRF
Click on Setup
Click on Group Conversion
Check CSV
Double click on any file in folder you select
It will group convert entire folder and put csv in same folder 

Thanks
Dr Bruce Kaiser
Chief Scientist
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Martins, Ana

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Mar 21, 2020, 3:47:12 PM3/21/20
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Hi!

Is P1XRF (V3.8.30 - version on the Bruker website) supposed to open the 5i files acquired with Artax?
I can't open mine to then convert to csv and preserve the metadata

thanks and apologies is this was already discussed but could find it in previous emails
hope you're all safe


all best and thanks in advance
ana
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Ana Martins
Conservation Scientist
The David Booth Conservation Department

The Museum of Modern Art
42 West 54th Street
New York, NY 10019   



MoMA is temporarily closed to help New York City and our global community curb the spread of the coronavirus outbreak. We care about everyone’s health and safety.

Aaron Shugar

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Mar 21, 2020, 4:43:53 PM3/21/20
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Hello Ana,

I hope you are well and staying healthy.  Bruker changed the 5i pdz file protocol and it comes in two forms - version 24 (the older pdz) and the new 25 (newer one you can only open in the newer artx and BIT).  On your XRF if you go into the utilities tab and I think output option, you can change it to 24 from 25, but that is only for the spectra saved on the XRF itself.  In the new artax, (if you are using that to collect your data) under the method editor, there is a new tab PDZ, here you can change the version to 24 as well and then all the spectra you save from there will be openable in s1pxrf or the older artax.
if you have saved files as version 25, you will need to convert those files to version 24.  Bruker had a software package for this called caltoolkit, but I don;t know if it was ever released officially. 
Hope that helps

Aaron

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Martins, Ana

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Mar 22, 2020, 12:15:49 PM3/22/20
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awesome!
thanks Aaron!
found and installed the Caltoolkit application and used the File Dump tab to convert to simple csv et voila!
saved all the data and metadata! I compared to the txt file saved from artax and data is ok!

best and stay healthy :)
ana




Alexander Seyfarth Mineralogical Analysis

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Mar 23, 2020, 1:58:23 PM3/23/20
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Hi

Hi Ana
The ARTAX SW (delivered with TRACER5i) can do this as well.
Which instrument are you talking about… as in any case the META DATA will be lost…(except for the file name).

Alexander




Alexander Seyfarth Mineralogical Analysis
Janesville USA



Vanessa Muros

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Mar 23, 2020, 4:21:57 PM3/23/20
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Hi Alexander,

Could you let us know how to do this in Artax?  I just checked through the different menu options on the version I"m using (8.00476 and can't remember if this is the one that came with the 5i or a later version) and see that there is an option in the Method Editor to save output as 24 or 25.  I am trying to create a new method to save data I already collected as v. 24 but keep getting an error message each time, so I must not be doing it correctly.

Is there somewhere else that we can do the conversion in Artax? And can it be applied to the spectra after it's been collected or does this mean for it to work you have to collect your data using Artax? 

thanks,
Vanessa








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Alexander Seyfarth Mineralogical Analysis

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Mar 23, 2020, 7:18:43 PM3/23/20
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Hi!

if you have cal toolkit you are good to go and can convert either version 24/25 to text 

in the ARTAX version i believe (as i did not use for 3 years) it would be “export/ all spectra” from the project you had loaded….

Suggest you get to rather play with CALTOOKIT and use BIT to acquire spectra :)
You can email direct if needed at asxray at charter dot net

Alexander




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