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FAIRmat-NFDI / nomad-measurements

A NOMAD plugin containing base sections for measurements.
https://FAIRmat-NFDI.github.io/nomad-measurements/
Apache License 2.0
12 stars 1 forks source link

Add XRF measurents #88

Open Pepe-Marquez opened 5 months ago

Pepe-Marquez commented 5 months ago

We have a couple of use cases of groups that are using XRF either as mapping or as a single measured point. We need a schema and parsers to cope with this. File formats should account for the tornado .spx format and for the files provided by the UIBK colleagues: https://fileshare.uibk.ac.at/d/1a200e720a29450f9add/ @hampusnasstrom, feel free to add info and comment on this. I believe there is already a reader for the .spx files. @RoteKekse, @yaruwangway, is there already a schema for Thomas's lab?

RoteKekse commented 5 months ago

Hey there is a parser which is quite user oriented. it takes the results of the data analysis and the spx files and reads position thickness and composition information

so proper schema should also include what model was used and other data :)

Pepe-Marquez commented 5 months ago

Hey there is a parser which is quite user oriented. it takes the results of the data analysis and the spx files and reads position thickness and composition information

so proper schema should also include what model was used and other data :)

I think starting with this would be already very good. Do you have a link to the parser @RoteKekse? This would be helpful for @fabianschoeppach to get inspired.

RoteKekse commented 5 months ago

ah fabian should know already but i can repost here: the parsing is done here:https://github.com/nomad-hzb/hzb-combinatorial-libraries-plugin/blob/main/src/hzb_combinatorial_libraries/schema.py#L131 the schema is here: https://github.com/nomad-hzb/nomad-baseclasses/blob/main/baseclasses/characterizations/xrf.py

keep in mind that i modified the schema right now in a way that elasticsearch is not over limit, since there are only 10000 values able to b eregistered per nomad entry my orginal schema was too much for 625 XRF spot measurements with 20 qunatites per measurements :D

fabianschoeppach commented 5 months ago

FYI: I created the branch '88-add-xrf-measurements' last week and did some work similar to the xrd stuff on there. I got the plugin and schema to run properly, e.g. I can use the create upload from schema. Still unsure about how to properly save the extracted data in the end.