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https://github.com/danporter/xmcd_analysis_example

Example data analysis of xas spectra from beamline i06 at Diamond Light Source.
https://github.com/danporter/xmcd_analysis_example

Last synced: 8 months ago
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Example data analysis of xas spectra from beamline i06 at Diamond Light Source.

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README 

          
# xmcd_analysis_example

Example data analysis of xas spectra from Diamond Light Source.



Includes generation of NeXus files with approximately the NXxas application definition,

where each file contains multiple channels (TEY, TFY) and multiple processing steps.

Example data is provided for the Fe-L3,2 edge in multiple sets of circular polarised 

XAS spectra from beamline i06-1. These spectra are processed to calculate the XMCD spectra.



 - Author: Dan Porter

 - Diamond Light Source Ltd

 - 2025



### Methodology

Scan files from a Synchrotron X-Ray beamline (I06-1 @ Diamond Light Source) are given in the data folder.

Each file is a fast, sweeping energy scan across the Fe L3,2 edge. The different files are for repeated

circular-right (CR) and circular-left (CL) polarisations (note the absolute direction is not known). 



Each scan file contains both electron-yield (TEY) and and fluorescence-yield (TFY) channels.



The code uses pythonic scan and spectra object models to make the analysis clearer (I hope!).



#### Channel Processing steps



For each channel, the following steps are performed:

 - normalise signal by monitor

 - normalise signal by flat pre-edge signal

 - fit a generic background (see below) including a step-edge for each absorption edge

 - subtract the background and normalise by the step height.



#### Averaging and Subtraction

Combining the background-subtracted channels from each scan:

 - interpolate the energy steps to provide consistent spectra

 - average the signals of the scans for each polarisation and channel

 - subtract the averaged signal CR - CL to calculate the XMCD

 - Integrate the XMCD spectra to determine the sum rules.



#### Background subtraction

Various background options are possible and several options are included in the code. 

The examples use an automatic fitted background composed of step models and a polynomial:



##### background = 

 - Step_1[cen=L3, wid=1-3eV, height=2/3 step height] + 

 - Step_2[cen=L2, wid=Step_1, height=1/3 step height] + 

 - Poly[order 3]



The step edges are initially chosen by looking for typical L-edges in the energy window.



More information about the background subtraction options is available in [xmcd_analysis_functions/spectra_analysis.py](xmcd_analysis_functions/spectra_analysis.py)



### Examples

The [xmcd_analysis_example.py](xmcd_analysis_example.py) script uses a suite of functions to generate the NXxas-like NeXus files and the final XMCD file.



The [xmcd_analysis_example.ipynb](xmcd_analysis_example.ipynb) jupyter notebook provides 

further explanation of the analysis steps and the Spectra object model used.



Note, all NeXus file links in the README can be clicked on to be viewed online using [myHDF5](https://myhdf5.hdfgroup.org/).



### NeXus Files

XAS energy scans converted into NeXus file with ~NXxas application definition.

Every scan measures both TEY and TFY channels, however the default mode is chosen as TFY.

Each scan has several processing steps. Each processing step is provided as an NXnote in the NXprocessing group, 

and has an associated NXdata containing the signal and background for both channels.



| Polarisation | Original Scan   | Converted Scan                                                                                                                                                                             |

|--------------|-----------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| CR           | data/236463.dat | [236463_nxxas.nxs](https://myhdf5.hdfgroup.org/view?url=https%3A%2F%2Fgithub.com%2FDanPorter%2Fxmcd_analysis_example%2Fblob%2F69a249b1bd51acb50412176e0512806be91b15f0%2F236463_nxxas.nxs) |

| CL           | data/236464.dat | [236464_nxxas.nxs](https://myhdf5.hdfgroup.org/view?url=https%3A%2F%2Fgithub.com%2FDanPorter%2Fxmcd_analysis_example%2Fblob%2F69a249b1bd51acb50412176e0512806be91b15f0%2F236464_nxxas.nxs) |

| CL           | data/236465.dat | [236465_nxxas.nxs](https://myhdf5.hdfgroup.org/view?url=https%3A%2F%2Fgithub.com%2FDanPorter%2Fxmcd_analysis_example%2Fblob%2F69a249b1bd51acb50412176e0512806be91b15f0%2F236465_nxxas.nxs) |

| CR           | data/236466.dat | [236466_nxxas.nxs](https://myhdf5.hdfgroup.org/view?url=https%3A%2F%2Fgithub.com%2FDanPorter%2Fxmcd_analysis_example%2Fblob%2F69a249b1bd51acb50412176e0512806be91b15f0%2F236466_nxxas.nxs) |

| CR           | data/236467.dat | [236467_nxxas.nxs](https://myhdf5.hdfgroup.org/view?url=https%3A%2F%2Fgithub.com%2FDanPorter%2Fxmcd_analysis_example%2Fblob%2F69a249b1bd51acb50412176e0512806be91b15f0%2F236467_nxxas.nxs) |

| CL           | data/236468.dat | [236468_nxxas.nxs](https://myhdf5.hdfgroup.org/view?url=https%3A%2F%2Fgithub.com%2FDanPorter%2Fxmcd_analysis_example%2Fblob%2F69a249b1bd51acb50412176e0512806be91b15f0%2F236468_nxxas.nxs) |

| CL           | data/236469.dat | [236469_nxxas.nxs](https://myhdf5.hdfgroup.org/view?url=https%3A%2F%2Fgithub.com%2FDanPorter%2Fxmcd_analysis_example%2Fblob%2F69a249b1bd51acb50412176e0512806be91b15f0%2F236469_nxxas.nxs) |

| CR           | data/236470.dat | [236470_nxxas.nxs](https://myhdf5.hdfgroup.org/view?url=https%3A%2F%2Fgithub.com%2FDanPorter%2Fxmcd_analysis_example%2Fblob%2F69a249b1bd51acb50412176e0512806be91b15f0%2F236470_nxxas.nxs) |



Each polarisation is measured 4 times. The background-subtracted spectra are averaged for each polarisation

and subtracted to provide the XMCD spectra, stored in a separate file. 

This NeXus file follows a similar structure to the NXxas files above, but also contains an NXnote in NXprocessing 

giving the integrated XMCD sum rules. 

Please note the methodology used for the sum rules here is not very accurate and needs refining.



 - [236464_nxxas.nxs](https://myhdf5.hdfgroup.org/view?url=https%3A%2F%2Fgithub.com%2FDanPorter%2Fxmcd_analysis_example%2Fblob%2F69a249b1bd51acb50412176e0512806be91b15f0%2Fxmcd.nxs)



### New NeXus Files (2025+)

An example of the new nexus files written directly from GDA on the beamline is provided, along with the processed

version. The new nexus files contain additional metadata and also contain a NXsubentry (`/entry/xas_entry`)

with application definition *NXxas*. These files trigger an autoprocessing ipython notebook that generates

the processed files and calculates XMCD. An example notebook is provided: [i10-1-37439_xas_notebook.ipynb](i10-1-37439_xas_notebook.ipynb).



| Filename                                                                                                                                                                         | Description                            | 

|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------|

| [data/i10-1-37436.nxs](https://myhdf5.hdfgroup.org/view?url=https%3A%2F%2Fgithub.com%2FDanPorter%2Fxmcd_analysis_example%2Fblob%2Fmaster%2Fdata%2Fi10-1-37436.nxs)               | RAW experiment data, CR polarisation   |

| [i10-1-37436_xas_notebook.nxs](https://myhdf5.hdfgroup.org/view?url=https%3A%2F%2Fgithub.com%2FDanPorter%2Fxmcd_analysis_example%2Fblob%2Fmaster%2Fi10-1-37436_xas_notebook.nxs) | Processed data, CR polarisation        |

| [data/i10-1-37439.nxs](https://myhdf5.hdfgroup.org/view?url=https%3A%2F%2Fgithub.com%2FDanPorter%2Fxmcd_analysis_example%2Fblob%2Fmaster%2Fdata%2Fi10-1-37439.nxs)               | RAW experiment data, CL polarisation   |

| [i10-1-37439_xas_notebook.nxs](https://myhdf5.hdfgroup.org/view?url=https%3A%2F%2Fgithub.com%2FDanPorter%2Fxmcd_analysis_example%2Fblob%2Fmaster%2Fi10-1-37439_xas_notebook.nxs) | Processed data, CL polarisation        |

| [37436-37439_xmcd.nxs](https://myhdf5.hdfgroup.org/view?url=https%3A%2F%2Fgithub.com%2FDanPorter%2Fxmcd_analysis_example%2Fblob%2Fmaster%2F37436-37439_xmcd.nxs)                 | Processed subtraction of polarisations |