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_sources/intro.md

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+# Welcome to PyXplore
+
+**PyXplore** is a modern, extensible toolkit designed for the high-throughput analysis and modeling of X-ray based data, including XRD (X-ray Diffraction), XPS (X-ray Photoelectron Spectroscopy), and EXAFS (Extended X-ray Absorption Fine Structure).
+
+This project empowers materials scientists and researchers to extract structural information, fit spectral profiles, simulate atomic arrangements, and visualize results — all in a reproducible, notebook-driven environment.
+
+---
+
+## 🔍 Key Features
+
+- ✅ **Peak Decomposition & Profile Fitting**: Based on WPEM (Whole Pattern fitting of powder X-ray diffraction by Expectation Maximum)
+- 🔬 **X-ray Spectrum Support**: XRD, XPS, and EXAFS workflows integrated
+- 🧪 **Amorphous & Crystalline Materials**: Suitable for mixed-phase materials and complex disordered states
+- 🧬 **Atomic Structure Simulation**: Support for solid solution models and local distortion
+- 📊 **Interactive Visualization**: Publication-quality plots, contour maps, and data exports
+- 📚 **Notebook-Based Tutorials**: Learn by doing with built-in step-by-step guides
+
+---
+
+## 📂 Documentation Overview
+
+This documentation is organized as a Book, with the following structure:
+
+- `parameter.md`: Overview of configuration options and input parameters
+- `ResultsFiles.md`: Output file types and their interpretations
+- `Tutorials/`: A complete collection of interactive notebooks for each use case
+- `references.bib`: Citation file for relevant academic work
+
+---
+
+## 🚀 Get Started
+
+To begin, navigate to the [Tutorials](Tutorials/index.md) section or explore the [parameter configuration](parameter.md) options.
+
+For any issues or contributions, feel free to open a GitHub issue or submit a pull request.
+
+Happy exploring with **PyXplore**!

_sources/parameter.md

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+
+# Parameters and Functions Documentation
+
+## Module: WPEM
+WPEM is the main call interface for diffraction refinement and analysis software, including various functions and subroutines for XRD analysis, background fitting, amorphous fitting, and more.
+
+### Author
+- **Bin CAO**  
+  Email: [bincao4-c@my.cityu.edu.hk](mailto:bincao4-c@my.cityu.edu.hk)  
+  GitHub: [https://github.com/Bin-Cao/PyWPEM](https://github.com/Bin-Cao/PyWPEM)
+
+---
+
+## Functions Overview
+
+### 1. `WPEMsolver`
+**From:** `EMBraggOpt.EMBraggSolver`  
+Solver for XRD profile refinement and analysis.
+
+### 2. `TwiceFilter`, `convert_file`, `read_xrdml`
+**From:** `Background.BacDeduct`  
+- **`TwiceFilter`**: Applies filtering techniques for background adjustments.  
+- **`convert_file`**: Converts XRD data files to the required format.  
+- **`read_xrdml`**: Reads `.xrdml` files for diffraction data.
+
+### 3. `Amorphous_fitting`
+**From:** `Amorphous.fitting.AmorphousFitting`  
+Fitting routine for amorphous phase diffraction data.
+
+### 4. `RadialDistribution`
+**From:** `Amorphous.QuantitativeCalculation.AmorphousRDF`  
+Calculates the radial distribution function (RDF) for amorphous materials.
+
+### 5. `Decomposedpeaks`
+**From:** `DecomposePlot.plot`  
+Decomposes diffraction peaks for detailed analysis.
+
+### 6. `XRD_profile`
+**From:** `XRDSimulation.Simulation`  
+Simulates XRD profiles for given crystal structures.
+
+### 7. `profile`
+**From:** `Extinction.XRDpre`  
+Generates XRD profiles with customizable parameters.
+
+### 8. `BgolearnOpt`
+**From:** `StructureOpt.SiteOpt`  
+Performs optimization for substitutional search and refinement.
+
+### 9. `XPSsolver`
+**From:** `WPEMXPS.XPSEM`  
+Solver for X-ray Photoelectron Spectroscopy (XPS) data refinement.
+
+### 10. `EXAFS`
+**From:** `WPEMXAS.EXAFS`  
+Performs Extended X-ray Absorption Fine Structure (EXAFS) analysis.
+
+### 11. `CrystalGraph`
+**From:** `GraphStructure.graph`  
+Generates crystal graphs for structural analysis.
+
+---
+
+## Executable Information
+
+### Execution Information
+- **Software Name**: WPEM (Diffraction Refinement Software)
+- **Author**: Bin Cao, Advanced Materials Thrust, Hong Kong University of Science and Technology (Guangzhou) ｜ Department of physics, City University of Hong Kong
+- **URL**: [https://github.com/Bin-Cao/WPEM](https://github.com/Bin-Cao/WPEM)
+- **Execution Time**: Dynamically generated at runtime.
+
+---
+
+## Key Functions
+
+### `XRDfit`
+#### Parameters:
+- **`wavelength`**: List of diffraction wavelengths.  
+- **`Var`**: Statistical variance of the background.  
+- **`Lattice_constants`**: Initial lattice constants for refinement.  
+- **`no_bac_intensity_file`**, **`original_file`**, **`bacground_file`**: Input data files.  
+- **`two_theta_range`**: Range of diffraction angles to analyze.  
+- **`density_list`**: Densities of crystals (optional).  
+- **`MODEL`**: Mode of analysis (`'REFINEMENT'` or `'ANALYSIS'`).  
+
+#### Returns:
+- Refined lattice constants, R-factor values, and runtime details.
+
+---
+
+### `BackgroundFit`
+#### Parameters:
+- **`intensity_csv`**: Input XRD data file.  
+- **`LFctg`, `lowAngleRange`, `bac_num`, `bac_split`**: Background filter parameters.  
+- **`window_length`, `polyorder`, `mode`**: Polynomial fitting settings.  
+
+#### Returns:
+- Background distribution statistics.
+
+---
+
+### `FileTypeCovert`
+#### Parameters:
+- **`file_name`**: Source file name.  
+- **`file_type`**: Format of the input file (`'dat'` or `'xrdml'`).  
+
+#### Returns:
+- Converted data.
+
+---
+
+### `Amorphous_fit`
+#### Parameters:
+- **`mix_component`**: Number of amorphous peaks.  
+- **`amor_file`**: Amorphous data file.  
+- **`ang_range`**: Angle range for refinement.  
+
+#### Returns:
+- Amorphous fit results.
+
+---
+
+### `CryGraph`
+#### Parameters:
+- **`folder_path`**: Path to save CIF files.  
+- **`BK_boundary_condition`**: Whether to apply Bon Kaman boundary conditions.  
+
+#### Returns:
+- Crystal structure graphs.
+
+---
+
+### Additional Functions
+- **`AmorphousRDFun`**: Computes radial distribution function for amorphous phases.  
+- **`Plot_Components`**: Visualizes decomposed XRD components.  
+- **`XRDSimulation`**: Simulates XRD patterns for given CIF files.  
+- **`CIFpreprocess`**: Processes CIF files for XRD analysis.  
+- **`SubstitutionalSearch`**: Conducts substitutional optimization searches.  
+- **`XPSfit`**: Fits XPS data for electron binding energy analysis.  
+- **`EXAFSfit`**: Performs EXAFS analysis for structural and bonding studies.
+

_sources/resultsFiles.md

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+
+# Results Files Documentation
+
+This page provides an overview of the output files generated by the **WPEM** software for diffraction refinement, background fitting, amorphous component analysis, solid solution modeling, and simulation tasks.
+
+---
+
+## General Information
+
+All results are saved in the **working directory** (`work_dir`), which can be specified by the user during execution. If not specified, outputs default to the current directory.
+
+### File Naming Conventions
+
+* **Prefix**: Indicates the task type (e.g., `XRD`, `Background`, `Amorphous`, etc.).
+* **Suffix**: Usually includes a timestamp to prevent file overwriting.
+
+---
+
+## Output Files by Function
+
+### 1. **Background Fitting**
+
+**Folder**: `ConvertedDocuments`
+
+* `bac.csv`: Fitted background intensities.
+* `no_bac_intensity.csv`: Diffraction signals after background removal.
+* `bac_points.csv`: Selected background points.
+* `intensity_fft.csv`: Diffraction signals processed by Fast Fourier Transform.
+* `de_backgroundfittingcurve.png`: Plot of the original data, fitted background, and background-subtracted signals.
+* `backgroundfittingcurve.png`: Visualization showing the raw data, selected background points, and the fitted background curve.
+
+---
+
+### 2. **XRD Refinement**
+
+**Folder**: `WPEMFittingResults`
+
+* `CrystalSystem0_WPEMout_<time>.csv`: Refined crystal information, including:
+
+  * `code`: Indicates Kα1 or Kα2 origin.
+  * `H`, `K`, `L`: Miller indices.
+  * `wi`, `Ai`, `L_gamma_i`, `G_sigma2_i`: Peak shape parameters (refer to the WPEM paper for details).
+  * `mu_i`: Peak positions.
+  * `intensity`: Peak intensities.
+  * `system0`, `system1`, etc.: Refers to different phases.
+* `hkl0_<time>.csv`: Diffraction indices for each peak in phase 0.
+* `WPEMfittingProfile_<time>.csv`: WPEM-generated fitting profile.
+* `WPEMPeakParas_<time>.csv`: Peak location and shape parameters, with profile fitting quality metrics.
+* `ResidualWPEM_fittingresult_<time>.png`: Plot comparing fitted results with experimental data.
+
+---
+
+### 3. **Amorphous Fitting**
+
+**Folder**: `DecomposedComponents`
+
+* `Amorphous.csv`: Extracted amorphous signals.
+* `M_Amorphous_componentsX.csv`: Identified amorphous peak components (X = index).
+* `upbackground.csv`: Updated background after amorphous subtraction.
+* `Decomposed_peaks.png`: Visualization of decomposed crystalline and amorphous components.
+
+---
+
+### 4. **CIF Parsing**
+
+**Folder**: `output_xrd`
+
+* `NAMEHKL.csv`: Calculated diffraction indices, angles, and theoretical intensities.
+* `NAME_Extinction_peak.csv`: List of extinction peaks caused by geometrical and systematic extinction.
+
+---
+
+### 5. **Solid Solution Modeling**
+
+**Folder**: `WPEMSitOpt`
+
+* `substitutional.png`: Fitting result of the optimized solid solution structure.
+* `DecompositionPlot.png`: Overlay of decomposed peaks and experimental data.
+
+---
+
+### 6. **XRD Simulation**
+
+**Function**: `XRDSimulation`
+
+* `Simulated_XRDPattern.csv`: Simulated XRD pattern based on the provided CIF file.
+* `SimulatedPeaks.csv`: Simulated peak positions and intensities.
+* `SimulationPlot.png`: Visualization of the simulated XRD pattern.
+
+---
+
+### 7. **CIF Preprocessing**
+
+**Function**: `CIFpreprocess`
+
+* `Processed_CIF_LatticeConstants.csv`: Extracted lattice constants from CIF.
+* `Processed_CIF_Structure.csv`: Atomic positions and unit cell parameters.
+* `ProcessedCIFPlot.png`: Visualization of the crystal structure.
+
+---
+
+### 8. **Substitutional Search**
+
+**Function**: `SubstitutionalSearch`
+
+* `SubstitutionalSearchResults.csv`: Possible substitutional configurations and their likelihoods.
+
+---
+
+### 9. **XPS Analysis**
+
+**Folder**: `XPSFittingProfile`
+
+* `XPSfittingProfile_<time>.csv`: Fitted XPS spectrum data.
+* `XPSPeakParas_<time>.csv`: Peak parameters including binding energies, areas, shapes, and fitting quality.
+* `WPEM_fittingresult.png`: Decomposed results of individual photoelectron peaks.
+
+---
+
+### 10. **EXAFS Analysis**
+
+**Folder**: `XAFS` / `WXAFS`
+
+* `FFT_EXAFS_unknown.png`: Radial distribution function representing local atomic structure.
+* `interactive_plot.html`: Interactive 2D wavelet transform visualization.
+
+---
+
+## Notes
+
+* All files are saved with descriptive names based on their function and timestamp.
+* Figures are generated in `.png` format for easy interpretation.
+* CSV files are widely compatible with data analysis tools such as Excel, Python, and MATLAB.
+
+For further reference and source code, please visit the [WPEM GitHub Repository](https://github.com/Bin-Cao/PyWPEM).
+

_sources/tutorials/EXAFS/7th.md

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+---
+jupytext:
+  formats: md:myst
+  text_representation:
+    extension: .md
+    format_name: myst
+    format_version: 0.13
+    jupytext_version: 1.11.5
+kernelspec:
+  display_name: Python 3
+  language: python
+  name: python3
+---
+
+# The tutorial 7th 
+Explains how PyXplore analyzes extended X-ray absorption fine structure (EXAFS) data.
+  
+## coding
+
+> **1. Save your XAS data to the root directory and rename the file to `absorb.csv`.**
+
+
+
+
+
+
+
+```{code-cell}
+# import PyXplore package
+from PyXplore import WPEM
+import pandas as pd
+
+WPEM.EXAFS('absorb.csv',de_bac = True).fit(first_cutoff_energy=22100,second_cutoff_energy=22400)
+```
+
+
+
+> **The result is saved in the `XAFS/EXAFS` folder.**
+

_sources/tutorials/XPS/8th.md

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+---
+jupytext:
+  formats: md:myst
+  text_representation:
+    extension: .md
+    format_name: myst
+    format_version: 0.13
+    jupytext_version: 1.11.5
+kernelspec:
+  display_name: Python 3
+  language: python
+  name: python3
+---
+
+# The tutorial 8th 
+
+Describes how PyXplore processes X-ray photoelectron spectroscopy (XPS) data.
+
+## coding
+
+> **1. Save your XPS data to the root directory and rename the file to `int.csv`.**
+
+
+
+
+```{code-cell}
+# import PyXplore package
+from PyXplore import WPEM
+import pandas as pd
+```
+
+> **2. Parse your diffraction data (`bing energy`, intensity) and perform background processing.**
+
+```{code-cell}
+intensity_csv = pd.read_csv(r'int.csv',header=None )
+var = WPEM.BackgroundFit(intensity_csv,segement=[[910,931],[948,952],[958,959],[966,970]],bac_num=120,Model='XPS',noise = 0.05,bac_var_type='multivariate gaussian')
+```
+
+> **3. After running the code, a new folder named `ConvertedDocuments` will be created in the root directory. This folder contains the background information.**
+
+> **Copy the two important files — `bac.csv` and `no_bac_intensity.csv` — from `ConvertedDocuments` into the root directory, as they are required for the next steps.**
+
+```{seealso}
+A key difference with XPS is that the initial binding energy needs to be queried and input using two parameters: `AtomIdentifier` and `satellitePeaks`.**
+```
+
+
+
+```{code-cell}
+
+AtomIdentifier = [['CuII','2p3/2',933.7,],['CuII','2p1/2',954,],]
+satellitePeaks = [['CuII', '2p3/2',941.6,],['CuII','2p3/2',943.4],['CuII','2p1/2',962.5,],]
+# The file name of non-background data 
+no_bac_intensity_file = "no_bac_intensity.csv" 
+# The file name of raw/original data 
+original_file = "int.csv"  
+# The file name of background data 
+bacground_file = "bac.csv"  
+
+# Execute the model
+WPEM.XPSfit(
+        var, AtomIdentifier, satellitePeaks,no_bac_intensity_file, original_file, bacground_file, 
+    bta = 0.80,iter_max = 50,
+)
+
+```
+
+
+
+> **The results are saved in the `XPSFittingProfile` folder.**
+

_sources/tutorials/amorphous/3rd.md

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+---
+jupytext:
+  formats: md:myst
+  text_representation:
+    extension: .md
+    format_name: myst
+    format_version: 0.13
+    jupytext_version: 1.11.5
+kernelspec:
+  display_name: Python 3
+  language: python
+  name: python3
+---
+
+# The tutorial 3rd 
+
+Provides a tutorial on analyzing amorphous signals.
+
+## coding
+
+> **1. Save your diffraction data to the root directory and rename the file to `intensity.csv`.**
+
+
+
+
+
+```{code-cell}
+# import PyXplore package
+from PyXplore import WPEM
+import pandas as pd
+```
+
+> **2. Parse your diffraction data (`2θ`, intensity) and perform background processing.**
+
+```{code-cell}
+intensity_csv = pd.read_csv(r'intensity.csv',header=None )
+var = WPEM.BackgroundFit(intensity_csv,lowAngleRange=3.8,poly_n=12,bac_split=8,bac_num=100)
+```
+> **3. After running the code, a new folder named `ConvertedDocuments` will be created in the root directory. This folder contains the background information.**
+
+> **Copy the two important files — `bac.csv` and `no_bac_intensity.csv` — from `ConvertedDocuments` into the root directory, as they are required for the next steps.**
+
+
+> **Parse the `.cif` file as demonstrated in the crystal fitting section, and generate the `peak0.csv` file.**
+
+
+
+
+
+
+```{code-cell}
+# The wavelength is set according to the actual light source
+wavelength = [1.03]
+# The file name of non-background data (2theta-intensity data)
+no_bac_intensity_file = "no_bac_intensity.csv" 
+# The file name of raw/original data (2theta-intensity data)
+original_file = "intensity.csv"  
+# The file name of background data (2theta-intensity data)
+bacground_file = "bac.csv"  
+
+
+# Input the initial lattice constants {a, b, c, α, β, γ}, whose values need to be assumed at initialization.
+Lattice_constants = [[17.53,17.53,6.47,90,90,120],]
+
+# Execute the model
+
+WPEM.XRDfit(
+    wavelength, var, Lattice_constants,no_bac_intensity_file, original_file, bacground_file, 
+    subset_number=3,low_bound=6,up_bound=16,bta = 0.78,iter_max = 50, asy_C = 0,InitializationEpoch=0, 
+    )
+```
+
+
+
+> After coverage, the amorphous components (referred to as "holes") are derived. You can visualize each amorphous hole using the provided plotting functions. The results are saved in the `DecomposedComponents` folder.
+
+```{code-cell}
+WPEM.Plot_Components(lowboundary = 4, upboundary = 19, wavelength = wavelength, Macromolecule = True,phase = 1)
+```
+
+
+```{seealso}
+For demonstration purposes, the code uses `iter_max = 5` to reduce computational cost. However, for practical applications, it is recommended to set `iter_max` to at least 50 for more reliable results.
+```
+