Sector Integration of 2D SAXS data

[Harshit Yadav]

Dear Jesse,

I am trying to perform sectorwise integration of 2D SAXS data but I cannot find any option for data integration. I tried looking into the documentation but can't find relevant information. 

I want to take a specific portion of the 2D image and then do integration to determine the corresponding 1D profile. Please let me know how to go about it.

Regards,

Harshit

[Jesse Hopkins]

Hi Harshit,

You’ll need to make a configuration file specific to your data. The tutorial you want is here:

https://bioxtas-raw.readthedocs.io/en/latest/tutorial/section3.html

To do a sector wise integration you’d need to mask the image so that only the sector of interest is integrated (either with a mask excluding the rest of the image, or an inverted mask that allows only what’s under it). If you want to do this for multiple sectors in an image you’d have to make multiple configuration files with different masks.

I hope that gets you started. Let me know if you have questions.

- Jesse

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Jesse Hopkins, PhD

Director

BioCAT, Sector 18

Advanced Photon Source

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[Harshit Yadav]

Dear Jesse,

Thank you for your help regarding radial averaging. 

I have an additional doubt regarding the profiles we get in the main plot. If I select the txt file where I have the data of intensity as a function of q, then I get a proper plot for my data. However, if I open the edf file for the same data, I get a weird pattern which is not representative of my data. I am confused as to why it happens. They are both from the same dataset, just in different format. This shouldn't make a difference to the plots but I think I am making some mistake while loading the data. I am attaching the plot for both cases. The yellow curve is from the edf file and the blue one is from the txt file.

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Regards,

Harshit

[Jesse Hopkins]

Hi Harshit,

The second image pretty clearly doesn't have a config file loaded. EDFs are image files, so you first need to generate an appropriate configuration file, and then you need to make sure that file is loaded when you load in the images.

The link I sent you previously contains information on generating a configuration file. Did you do that for your data? Note that the configuration file is going to be different for every experiment, you can't use the one from the tutorial for your data, you need to carry out the steps with your own calibration measurements (e.g. silver behenate measured on your setup).

All the best.

- Jesse

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Jesse Hopkins, PhD (he/him)
Director, BioCAT
Sector 18, Advanced Photon Source
Research Associate Professor, Illinois Tech

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