reixs 0.0.17

Library to analyse, plot, and export data taken at the REIXS Beamline at the Canadian Light Source, Saskatoon, Canada.

CLS REIXS Analysis

This is a library to analyse, plot, and export REIXS beamline data. The package is meant to provide a framework to load data into jupyter and enable data interaction.

Further beamline information is available on the Website of the Canadian Light Source.

Installation

Install the package from PyPi with the pip package manager. This is the recommended way to obtain a copy for your local machine and will install all required dependencies.

    $ pip install reixs

You will also need Jupyter Notebook together with python 3 on your local machine.

In case that certain widgets aren't rendered properly, make sure to enable the appropriate jupyter extensions

    $ jupyter nbextension enable --py widgetsnbextension

Running

Launch your local jupyter installation with

    $ jupyter notebook

Examples

Load the required module

Before you start, you will need to import the required reixs package, enable bokeh plotting, and set the base directory.

## Define base directory
basedir = "/home/braun/ownCloud/Beamtime/example_data/"

## Setup necessarry inputs
from reixs.LoadData import *
from bokeh.io import show, output_notebook
output_notebook(hide_banner=True)

1d plots

General Loader1d

sca = Load1d()
sca.load(basedir,'FileName.dat','x_stream','y_stream',1,2,3,4,norm=True)
sca.addScans(basedir,'FileName.dat','x_stream','y_stream',1,2,3,4,norm=False,avg=False)
sca.subtractScans(basedir,'FileName.dat','x_stream','y_stream',1,2,3,4,norm=False,avg=False)
sca.plot()
sca.exporter()

1. Specify the variable for the base directory (basedir)

2. Enter the file name of the scan to analyse ('FileName.dat')

3. Options for x_stream quantities include:

• All quantities in the header file
• Mono Energy for the excitation energy
• MCP Energy (uncalibrated)
• SDD Energy (uncalibrated)
• XEOL Energy (uncalibrated, actually the wavelength scale)
• Points (by index)

4. Options for y_stream quantities include:

• All quantities in the header file
• TEY (Total Electron Yield: sample normalized by mesh)
• TFY (Total Fluorescence Yield, normalized by mesh)
• PFY and iPFY (Partial Fluorescence Yield and Inverse Partial Fluorescence Yield, both normalized by mesh) Specify ROI with brackets, either by XAS edge or energy: e.g. PFY[O] for PFY at the O K edge e.g. PFY[490:560] for PFY from 490eV to 560eV
• specPFY (spectrometer PFY, normalized by mesh) specify energy range e.g. specPFY[500:520]
• XES and rXES (X-Ray emission and resonant x-ray emission at selected energies from the spectrometer MCP data) e.g. rXES[560:565]
• XRF and rXRF (X-Ray fluorescence and resonant x-ray fluorescence at selected energies from the SDD data) e.g. rXRF[550:570]
• XEOL and rXEOL (XEOL data from the optical spectrometer)
• POY and TOY (Partial optical yield and total optical yield, normalized by mesh) e.g. POY[300:750]

5. List all scans to analyse (comma-separated)

6. Set optional flags. Options include:

• norm (Normalizes to [0,1])
• xcoffset (Defines a constant shift in the x-stream)
• xoffset (Takes a list of tuples and defines a polynomial fit of the x-stream)
• ycoffset (Defines a constant shift in the y-stream)
• yoffset (Takes a list of tuples and defines a polynomial fit of the y-stream) e.g. offset = [(100,102),(110,112),(120,121)]
• background (Subtracts a XEOL background from XEOL scans)
• energyloss (Requires the incident photon energy and moves the resultant MCP scale to energy loss)

Absorption Scans

xas = XASLoader()
#xas.load(basedir,'Plate2a.dat','TEY',1,4,6,norm=True)
#xas.load(basedir,'Plate2a.dat','PFY[O]',1,4,norm=True)
xas.add(basedir,'Plate2a.dat','PFY[O]',1,4,norm=False,avg=False)
xas.subtract(basedir,'Plate2a.dat','PFY[O]',1,4,6,norm=False,avg=False)
xas.plot()
xas.exporter()

Emission Scans (MCP)

xes = XESLoader()
# Options: XES, rXES
xes.load(basedir,'Plate2a.dat','XES',3,xoffset=[(510,520)])
xes.load(basedir,'Plate2a.dat','XES',3)
xes.load(basedir,'Plate2a.dat','rXES[520:560]',4)
xes.add(basedir,'Plate2a.dat','XES',1,4,)
xes.subtract(basedir,'Plate2a.dat','XES',1,4)
xes.plot()
xes.exporter()

XRF Scans (SDD)

xrf = XRFLoader()
# Options XRF,rXRF
xrf.load(basedir,'Plate2a.dat','XRF',3,xoffset=[(510,520)])
xrf.load(basedir,'Plate2a.dat','XRF',3)
xrf.load(basedir,'Plate2a.dat','rXRF[520:560]',4)
xrf.add(basedir,'Plate2a.dat','XRF',1,4,)
xrf.subtract(basedir,'Plate2a.dat','XRF',1,4)
xrf.plot()
xrf.exporter()

XEOL Scans

xeol = XEOLLoader()
#Options: XEOL, rXEOL
xeol.load(basedir,'RIXS_ES_QA.dat','XEOL',1,2,3,4,background=3)
xeol.plot()

2d Images

Note: Can only load one scan at a time!

load2d = Load2d()
load2d.load(basedir,'Plate2a.dat','Mono Energy','SDD Energy','SDD',1)
load2d.plot()
load2d.exporter()

EEMs (normalized by mesh current)

Note: Can only load one scan at a time!

eems = EEMsLoader()
eems.load(basedir,'Plate2a.dat','SDD',1)
eems.load(basedir,'Plate2a.dat','MCP',1)
eems.load(basedir,'RIXS_ES_QA.dat','XEOL',2,background=3)
eems.plot()
eems.exporter()

Mesh Scans

mesh = LoadMesh()
mesh.load(basedir,'mesh_scan.txt','Y','Z','TEY',24,norm=True)
mesh.plot()
mesh.exporter()