wtEXAFS

Version: 0.2.1

Last update: 2023/05/05

wtEXAFS is an Windows GUI for wavelet transformation of EXAFS

Prerequisites

It is highly recommended to create a new environment in PyCharm to run wtEXAFS.

Windows10 x64
Python >= 3.7
matplotlib == 3.5.1
numpy == 1.21.5
pywin32 == 303

How to start

It is noted that wtEXAFS needs to run on Windows 10 (x64).

For python users

If git is existed, simply clone the repository:

git clone https://github.com/Himmelspol/wtEXAFS.git

Otherwise, download the ZIP file of the repository and unzip it.

1. Start from Python

Download Python (64-bit) from https://www.python.org/downloads/
Select "Add Python 3.X to PATH" and install Python with "Customize installation" mode
On "Advanced Options" page, choose "Install for all users" and install
After successful installation, press Win + R and open command line window (cmd), then change directory to where " wtEXAFS" resides, for example:
```
 D：
 cd D:\test\wtEXAFS
```
Install requirements in cmd as following:
```
 pip install -r requirements.txt
```
Run "main.py" in cmd as following:
```
 python main.py  
```

2. Start from PyCharm

Open the project "wtEXAFS"
Set python interpreter (python version: >= 3.7.9)
Install requirements if necessary
Run "main.py" in the root directory to use the GUI

Start from Windows executable file (.exe):

Download the packaged files from (one of the three):
1. Google drive: https://drive.google.com/drive/folders/1wctfzMaA-KoCo6_diqWzBwc80WCeka35?usp=sharing
2. MEGA: https://mega.nz/folder/wMgnRCAD#Jv1gsYz5vHrjq1Nprh6VJA
3. Baidu cloud: https://pan.baidu.com/s/1tvUyJV1Vec3nzR2bw19wLw code:m8o4
There are two types of file on the cloud:
1. Download wtEXAFS-XXX.zip, unzip it, find wtEXAFS.exe in the folder and double-click to run
2. Download wtEXAFS-XXX.exe, double-click to run (relatively slow)

How to use

See guide_for_wtEXAFS.pdf for more details.

1. Import chi(k) data

1.1 Single file mode:

Open *.txt/.chi file containing at least two column, one column is k, the other column is chi(k):
```
#-------------------------------------
#  k   chi 
   0   0.0001
   0.5 0.0002
```
*.chi file (.chi/.chi1/.chi2/.chi3) is a kind of EXAFS output file extracted from ATHENA (https://bruceravel.github.io/demeter/documents/Athena/index.html)
In this mode, the user can specify in the input box the row where the data starts and the column where k, chi( k) resides
Select Confirm and show selected data to refresh content display box
Select Continue and close this window

1.2 Multiple column mode

Only open *.chi file containing at least two column, one column is k, the other columns are different chi(k)
In this mode, the user can specify in the input box the row where the data starts and the column where k, chi( k) resides. For chi(k) column, enter SPACE to separate different column:
```
# The numbers below represent different columns
3 4 5 6 7 8 9
```
Other operations are the same as Single file mode

2. k-weight selection

If the imported data itself is k-weighted (e.g., k^3chi(k)), select k-weight to 0
If the imported data is not k-weighted, select k-weight from 1, 2, and 3
Click Accept k-weight and then the user can Show k-weighted data
Click Next step for next step

3. Custom wavelet transform parameters

Enter kmin/kmax/dk, Rmin/Rmax/dR in the input box
Enter Sigma/Eta in Morlet wavelet input box and then Accept it
Or Enter n in Cauchy wavelet input box and then Accept it
Then the user can Show wavelet
NOTICE:
- kmin and kmax must be within the data range
- Rmin must be > 0
- Sigma and Eta must be > 0
- n must be > 1
- if not sure, default value is ok
- If the input dK does not match the imported data, interpolation will be automatically performed

4. Start wavelet transformation

Click Start WT to start calculation (usually takes 3 to 5s)
Then the user can Show WT result or Save WT result

The output file is a TXT file, with internal structure as following:

# k_value R_value wavelet_coef(column3) wavelet_coef(column4) ...# This line will not display in the *.txt
  0.00000 0.50000 0.013305 0.012805
  0.05000 0.50000 0.013314 0.012963
  0.10000 0.50000 0.013400 0.013002

If needed, Click Start inverse WT to reconstruct EXAFS spectra according to wavelet type and WT result

NOTICE:
- If multi-column mode was usd, only one spectral result can be displayed at a time. And the user can choose which one to display

About author

Hi everyone, I am a beginner of XAFS and Python, and I noticed that there are not many GUI for EXAFS wavelet transformation yet. Thus, with the purpose of learning, I wrotethis GUI and hope it can help others :)

EXAFS is a powerful technique for detecting the local structure of different materials. Actually, EXAFS is a composite signal of electron waves, which is well suited for analysis using wavelet transform. Although it is difficult to gain quantitative results from wavelet transformation of EXAFS signal, wavelet transformation can still give more information to help us carry out k-space LCF, EXAFS modeling and so on.

References

Ravel B. and Newville M. (2005) ATHENA, ARTEMIS, HEPHAESTUS: Data analysis for X-ray absorption spectroscopy using IFEFFIT. J. Synchrotron Radiat. 12, 537–541.
Munoz M., Argoul P. and Farges F. (2003) Continuous cauchy wavelet transform analyses of EXAFS spectra: A qualitative approach. Am. Mineral. 88, 694–700.
Funke H., Scheinost A. C. and Chukalina M. (2005) Wavelet analysis of extended x-ray absorption fine structure data. Phys. Rev. B - Condens. Matter Mater. Phys. 71, 1–7.
Funke H., Chukalina M. and Scheinost A. C. (2007) A new FEFF-based wavelet for EXAFS data analysis. J. Synchrotron Radiat. 14, 426–432.
Timoshenko J. and Kuzmin A. (2009) Wavelet data analysis of EXAFS spectra. Comput. Phys. Commun. 180, 920–925.
Xia Z., Zhang H., Shen K., Qu Y. and Jiang Z. (2018) Wavelet analysis of extended X-ray absorption fine structure data: Theory, application. Phys. B Condens. Matter 542, 12–19.
Arts L. P. A. and van den Broek E. L. (2022) The fast continuous wavelet transformation (fCWT) for real-time, high-quality, noise-resistant time–frequency analysis. Nat. Comput. Sci. 2, 47–58.
https://www.esrf.fr/UsersAndScience/Experiments/CRG/BM20/Software/Wavelets
http://perso.u-pem.fr/farges/wav/
https://github.com/hellozhaoming/wtexfas
https://github.com/wangmiaoX/wavelet-transform-exafs
http://en.volupedia.org/wiki/Convolution

supperpojke/wtEXAFS