Prerequisites

• Access to S3DF
• An X11 client installed on your computer
  • MacOS: XQuartz
  • Windows: MobaXterm
• Request permissions to access the data

S3DF

Data is stored on S3DF, access via ssh with your username and password

ssh -X <yourusername>@s3dflogin.slac.stanford.edu

From the S3DF login node, ssh to iana which will allow you to use MATLAB for analysis and mounts the data volumes

ssh -X iana

Then cd to the data directory

cd /sdf/group/ssrl/dsokaras/bl6-2a/tender_data

Load MATLAB

module load matlab

Open MATLAB with the gui

matlab &

The main analysis scripts/commands are:

• onepotRIXS: analyzes/combines all RIXS scans to give HERFD XAS
• onepot: analysis for a single .sif file
• tender_ana.mlx: MATLAB live notebook for analyzing/averaging XES

onepotRIXS and onepot

In the MATLAB CLI, add the paths for the analysis scripts (onepot, onepotRIXS, various sif tools, etc)

addpath /sdf/group/ssrl/dsokaras/bl6-2a/tender_data/Analysis/MATLAB 
addpath /sdf/group/ssrl/dsokaras/bl6-2a/tender_data/Analysis/MATLAB/sifFiles/ 

Run the analysis script onepotRIXS. The '*' wildcard grabs all files at the various energies for a given scan for analysis.

onepotRIXS('Fe2PdtCO6_Toluene_40mMol_SKa_RIXS_01*')

The analysis writes .mat, .fig and .pdf files and open the plots: ![[onepotrixs.png]] You can call onepotRIXS specifying the pixel range and central pixel (y-value) and it will add the HERFD plot to the TFY plot

• Note: You will need to close the figure window and then rerun onepotRIXS and it will open the window with the HERFD XAS plotted.

onepotRIXS('Fe2PdtCO6_Toluene_40mMol_SKa_RIXS_01*', 5, 1065)

![[herfd.png]] This will also write an "extract_*.txt" file with the energy, HERFD and TFY columns. ![[extract_file 1.png]] For a single .sif file use onepot:

onepot("filename.sif", "bcg", "filename_dark.sif", "extract", true, "Treshold", thresholds)

• Note: thresholds is optional. It is spelt wrong. It is an array. Extract is optional. To select a range of images use scanNumbers with array [start:stop]:

onepot('Mo4_concentrated_MoL3val_2525.75eV_01.sif', 'bcg', 'Mo4_concentrated_MoL3val_2525.75eV_01.sif', 'scanNumbers', [31:60], 'extract', true)

Tender_ana.mlx

This is a live script is wrapper for the onepot scripts and averages XES data. To run the script update the path to the data which is stored as the fol variable. The script will output the averaged XES data for the various emission lines and write the data a to txt file. ![[tender_ana.png]]

Other commands

Opening old figures:

fig = openfig('YOURFIGFILE.fig')

For loading and saving old data:

load 'yourfile.mat'
save('newfile.txt', 'var1, 'var2', ..., '-ascii')