Creating Header file for analysis using Bruker Nanostar

[Shruti Sharma]

Hi,

I am using RAW for analyzing the data from SAXS experiments performed using Bruker Nanostar, Vantec-2000 detector on Ni alloys. In order to create a configuration file, I want to write my own function to load the header file and add it to RAW for this particular detector. 

I was hoping if you could help me with this. 

[Jesse Hopkins]

Hi Shurti,

Sure, I can help with that. If you'd like to write it yourself, the specifications are pretty simple:

1) The function takes a single input, the filename of the image file that you're loading the header for.

2) The function returns a single dictionary, where the keys are the header items (things like 'Date', 'Beamstop Counts', 'Flux', etc) and the values are the value of those items in the header file. The dictionary keys should be strings, the dictionary values can be any type, but if you're going to use them for normalization they should be something that python can cast as a float.

3) Add your new function as a header type in the all_header_types dictionary on line 915 of the SASFileIO.py file.

You can see examples of these loading functions in the SASFileIO.py file starting around line 418.

Once you've written it, send it to me and I can include it in releases of RAW going forward.

Alternatively, if you send me an example dataset with images and associated header files, and an explanation of the file format, so I know what to load, I can write the load function for you when I have time, and include it in the subsequently released version of RAW.

All the best.

- Jesse

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Jesse Hopkins, PhD

Beamline Scientist

BioCAT, Sector 18

Advanced Photon Source

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[Shruti Sharma]

Hi Jesse,

Thanks for your reply. I would definitely give this a try but in the meantime, if you could help me with the function, that would be great! Please find attached the grfm files taken for AgBe, water, background (as in no sample or Kapton tape), Kapton tape, and a Ni alloy. The files contain all the information that can be retrieved by opening the gfrm file with a binary (HEX) data viewer. Additionally, for reference, the beam center coordinate is (1029, 1024.5). The detector is Vantec-2000, 2048 x 2048 pixels, pixel size 68 um x 68 um, and the sample-to-detector distance is 1080.4mm.

Kindly let me know if anything else is needed from my end.  

Thanks again,
Shruti

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Thanks and Regards,

Shruti Sharma
Ph. D. Candidate
Department of Materials Science and Engineering
Arizona State University
Tempe

Mobile: +1-6234284684 
ssha...@asu.edu

[Jesse Hopkins]

Hi Shruti,

When you said you wanted to read in a header file, I assumed you were referring to a separate file with additional information about the experiment (often: incident intensity, exposure time, etc). There isn’t such a file in the data you provided. It seems like you’re actually interested in reading the header information of the image file and using that in RAW? What information exactly do you want to get of the image header?

All the best.

- Jesse

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Jesse Hopkins, PhD

Beamline Scientist

BioCAT, Sector 18

Advanced Photon Source

To view this discussion on the web visit https://groups.google.com/d/msgid/bioxtas_raw/CAPppEN4NeaoXfhFWXDW_iHSZu8eSKLccbb1kmTDeqyH6KZccAg%40mail.gmail.com.
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