Examples

This section contains practical examples and Jupyter notebooks demonstrating CDIutils functionality.

Example Notebooks

• BCDI Pipeline
  • A Notebook to Run the BcdiPipeline Instance
  • Main Parameters
  • Phase Retrieval GUI
  • Analyse the phasing results
  • Optionally, generate a support for further phasing attempts
  • Selection of the best reconstructions & mode decomposition
• Interactive Features in cdiutils
  • Installation
  • plot_3d_isosurface
  • ThreeDViewer Class
  • Notes
  • TabPlotData Class
• BCDI Reconstruction Analysis
  • 1. Setup and Initialisation
  • 2. Visualise and Compare Datasets
  • 3. Comparing Reciprocal Space Data
  • 4. Advanced Analysis (customisable)
  • 5. Next Steps
  • Feedback and Support
  • Credits
• CXI File Browser
  • Set up the file path
  • Basic usage
  • View hierarchical structure
  • Search functionality
  • Display specific datasets
  • Interactive exploration
  • Closing the explorer
  • Using context manager
  • Direct use of CXIFile class
  • Load data from a CXI file
  • Credits
• Pole figure notebook example
  • Usage of cdiutils.analysis.pole_figure

Jupyter Notebook Examples

The following Jupyter notebooks provide hands-on examples of CDIutils usage:

Interactive 3D Visualisation

Download: interactive_features.ipynb

New in v0.2.0! Learn to use the modern interactive 3D visualisation tools:

• plot_3d_isosurface - Quick interactive isosurface plotting with multiple quantities

• ThreeDViewer - Widget for exploring complex 3D arrays (amplitude + phase)

• TabPlotData - Interactive browser for CDI reconstruction results

• Colormap selection and colorbar control (auto-scale, symmetric, manual limits)

• NaN handling for clean visualisations

• Theme toggle and rotation animations

BCDI Pipeline Example

Download: bcdi_pipeline_example.ipynb

Complete end-to-end pipeline This comprehensive example demonstrates a full BCDI analysis workflow:

• Setting up and running the BcdiPipeline class

• Automated data processing and phase retrieval

• Post-processing and strain analysis

• Interactive 3D visualisation with plot_3d_isosurface (new in v0.2.0)

• Advanced plotting and figure generation

This example showcases the complete workflow from raw data to publication-ready visualisations, including the new Plotly-based interactive 3D plots.

BCDI Reconstruction Analysis

Download: bcdi_reconstruction_analysis.ipynb

This notebook demonstrates comprehensive BCDI reconstruction analysis including:

• Loading experimental data

• Phase retrieval with PyNX

• Post-processing and strain analysis

• Visualisation and interpretation

CXI File Exploration

Download: explore_cxi_file.ipynb

Learn how to:

• Navigate CXI file structure

• Extract reconstruction results

• Analyse metadata and experimental parameters

• Export data for further processing

Pole Figure Analysis

Download: pole_figure.ipynb

This example covers:

• Stereographic projection analysis

• Crystal orientation mapping

• Pole figure generation and interpretation

• Advanced crystallographic analysis

Template Notebooks

Ready-to-use templates are available in the templates directory:

• bcdi_pipeline.ipynb - Complete BCDI analysis pipeline

• step_by_step_bcdi_analysis.ipynb - Detailed step-by-step reconstruction

• detector_calibration.ipynb - Detector calibration procedures

Getting Started

1. Download the notebook examples above

2. Install CDIutils following the Installation guide

3. Run the notebooks in your Jupyter environment

4. Adapt the examples to your specific datasets