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Python-tools

Data Analysis Tools for X-ray Spectroscopy

Table of Contents

Larch XAS.py

Citation: M. Newville, Larch: An Analysis Package For XAFS And Related Spectroscopies. Journal of Physics: Conference Series, 430:012007 (2013).

Install

  • Download Anaconda
  • Download athena_project.py and put it at the same folder with Larch_XAS.py

Within a shell:

  1. Activate your conda environment (called base by default) and update it:
conda activate
conda update -y conda python pip
  1. (optional/expert) Create a dedicated environment for Larch and activate it:
conda create -y --name xraylarch python==3.9
conda activate xraylarch
conda update --all
  1. Install main dependencies:
conda install -y "numpy=>1.20" "scipy=>1.6" "matplotlib=>3.0" scikit-learn pandas
conda install -y -c conda-forge wxpython pymatgen tomopy pycifrw
  1. Install Larch (latest release):
pip install xraylarch
  1. Set Conda Environment by changing Python Interpreters as Anaconda\envs\xraylarch\python.exe

Usage

Data processing

If merging fluorescence scans (e.g. BNL NSLS-II BMM)

FILE_TYPE = '.prj'

If merging single scan (e.g. BNL NSLS-II BMM)

FILE_TYPE = ''

If merging transmission scans (e.g. BNL NSLS-II ISS)

FILE_TYPE = '.dat'

If plotting scans file exported from Athena

FILE_TYPE = '.txt'

'Auto' is default to process the transmission data based on the notation in the raw file; Otherwise True or False to decide what type of data you want to export (transmission or fluorescence scans). True for transmission scans; False for fluorescence scans

TRANSMISSION_MODE = 'Auto'

Copy and paste the directory of the data folder

INPUT_PATH = r'D:\Research data\SSID\202209\20220330 ISS NbOx'

Data display (optional)

Add scan name you want to exclude

SKIP_SCANS = ['MnO2_45_16C_Charge_Mn_001']

Do normalization for fluorescence scans

IF_NOR = False

Add plus and minus standard deviation lines for fluorescence scans

ADD_DEV = False

Display Athena parameters, such as atomic symbol, edge, label, etc.

SHOW_DATA_INFORMATION = False

Plot spectrum (optional)

  • Download larch_plot_config.ini
  • Paste the absolute directory of larch_plot_config.ini in Larch_XAS.py file
CONFIG_FILE = r"D:\Research data\SSID\202205\20220509 20210221 BMM\b28_Sc_pure_config.ini"
  • Update the config file.

The key parameters:

sample_list = [0, 1]
standard_list = [0]
sample_label = ['Pure Sc', 'NbAlSc']
energy_range = (4425, 4625)
if_save = True      # True or False to save the plot
output_filename = 'Sc-b33-NbAlSc-SP'

CFNXRD2Jade.py

Usage

  • Paste your data directory
INPUT_PATH = r"D:\Research data\SSID\202205\20220526 XRD b31 NbAl"
  • Set up your plotting parameters
FILE_TYPE = '.xy'
PLOT_LIST = [5, 3]                      
SAMPLE_LABEL = ['On Sapphire', 'On Fused Silica']                   
OUTPUT = False                      
Y_RANGE = (-100, 500)               
PLOT_OFFSET = 500                   
FRAMELINEWIDTH = 2
LINEWIDTH = 2
IF_SAVE = True                    
IF_LEGEND = True                   
LEGEND_LOCATION = 'upper left'
PALETTE = pld.Spectral_4_r          
CMAP = PALETTE.mpl_colormap         
OUTPUT_FILENAME = 'b34 - MoTiCu - 800C30M'

plot xrd SSID insitu.py

Size Limit CLI

Usage

Copy and paste data location

INPUT_PATH = r'D:\Research data\SSID\202204\20220406 XPD ex-situ check\LK_b30-14_Nb40Al60Sc_SiO2Si_pristine_heating'

Absolute directory or ' ' will return index as the color bar

TIMESTAMP_FILE = 'sample_LK_heating_20220408_172022.xlsx'

[ ] for default or [1, 7, 5, 3] index list for the index sequence you desire

PLOT_LIST = list(np.arange(0, 191, 5))

Number you want to add to an offset for each curve

PLOT_OFFSET = 0.5

"True" if you want to show the plots

PLOT_FIGURE = True

"True" if you want to save the converted file

SAVE_IMG = False

CMS GIWAXS and GISAXS.py

Usage

  • Download CMS_plot_config.ini
  • Paste your data directory in the CMS_GIWAXS_and_GISAXS.py
INPUT_PATH = r"D:\Research data\SSID\202302\20230228 CMS b33 SP\saxs\analysis\qz=0.07_dq=0.02_b33"
  • Paste your CMS_plot_config.ini absolute directory
CONFIG_FILE = r"D:\Research data\SSID\202302\20230228 CMS b33 SP\saxs\b33-NbAlSc-SP-th0.2_CMS_plot_config.ini"
  • Update the config file for your data plot.

The key paramteres:

sample_list = [0, 1]
angle_range = 'wide' or 'small'
sample_label = ['Pristine', 'Heated']
output_for_jade = False or True    # Converted file for Jade reading
output_filename = 'b33-NbAl and Sc-SP-th0.2'
if_save = True or False     # Save the plot

CMS SAXS data export

  • Download SciAnalysis folder
  • Open saxs\analysis\runXS.py
  • Paste the directory of the SciAnalysis folder
SciAnalysis_PATH=r"D:\Research data\SSID\Advanced Computer Python\Python-tools\SciAnalysis"
  • Update the protocols command to reduce 2D scattering data
protocols = [Protocols.linecut_qr(name='qz=0.07_dq=0.02_b33', qz=0.07, dq=0.02, xlog=False, ylog=True, show_region=True, gridlines=True, plot_range=[0.004, None, 1, None])]

name: Exported folder name

qz: Integration center along qz direction

dq: Integration range

plot_range: [x1, y1, x2, y2]

License