Package: quantorxs
QUANTORXS is an open-source program to automatically analyze XANES
spectra at Carbon, Nitrogen and Oxygen K-edges edges to quantify the
concentration of functional groups and the elemental ratios (N/C and
O/C). It is based on a novel quantification method published inAnalytical
chemistry.QUANTORXS performs the following tasks automatically:Load the data from the file(s)Remove backgroundNormalize the spectraGenerate a model of the fine structure a fit it to the experimental
dataCalculate the functional groups abundances and elemental rations from
the results of the fitGenerate an Excel file and multiple figures with the results and
normalised spectra files.This is illustrated in more detail in the following diagram:Alt textQUANTORXS is designed to work without any user input other than the
experimental spectra. Users willing to modify the details of the
quantification can download the code from itsGitHub
repository.The code was initially written byCorentin Le
Guillou.Francisco de la
Peñacreated the command line and graphical user interfaces.Installing QUANTORXS.QUANTORXS is written in the Python programming languague and is
available frompypi. It runs in
any operating system with the Python programming language installed.To install QUANTORXS execute the following in a terminal:pipinstallquantorxsStep-by-step installation instructions for Windows usersIf you are new to Python we reccomend you to install the opensource and
freeAnaconda Python
distributionfor your platform
first. Afterwards, from the Microsoft WindowsStart Menu, open
“anaconda prompt” as in the image below:Alt textThen type the following and pressEnter(requires connection to the
internet):pipinstallquantorxsAlt textThat’s all! QUANTORXS should now be installed in your system.Starting the QUANTORXS Graphical User InterfaceTo start the graphical interface execute thequantorxs_guie.g. a
terminal. Alternatively, Windows users can start it by searching for the
executable file “quantorxs_gui” in theStart Menuand launching it
as shown in the image below.Alt textHow to use the graphical interfaceThe program is designed to process several spectra at once. All source
spectra should be assembled in one folder. QUANTORXS reads only the
format produced byaXis2000Click on theChoose data directorybutton and select the folder
containing the source spectra.Type in an output folder name (relative to the data directory) to
store the results of the analysis. The default isQUANTORXS results.Make sure that thedemobox is not checked. If checked, it uses
default files as input to produce an example of the output files.Select the format of the figure output (the default is SVG)Set theoffsetif required to compensate from any energy
misalignment (e.g. from poorly calibrated monochromator)common to
all spectra.Click theRunbutton and wait until the analysis is completed
(usually a few secondes per spectrum).Alt textDescription of the output filesThe output folder will be created in the folder from which the data have
been taken. An .xls result file and two different sub-folders are
created:a .xls file contains several sheets:The fitting parametersThe quantified data (aromatic, ketones, aliphatics, carboxylics; as
well as N/C and O/C ratios) and some related plotsThe spectra at the C-K edge normalized by the area ratio methodThe spectra at the N-K edge normalized by the area ratio methodThe spectra at the O-K edge normalized by the area ratio methodThe fitted heights of the Gaussians for the area-based normalization
at the C-K edgeThe fitted heights of the Gaussians for the area-based normalization
at the N-K edgeThe fitted heights of the Gaussians for the area-based normalization
at the O-K edgeAlt textAlt textAlt textAlt textA folder containing the .txt files of each normalized spectrumA folder with figures displaying:The cross-section fitThe normalized spectraThe deconvolution (all gaussians included)