User Guide

Comprehensive guides for using CDIutils in your BCDI experiments.

Core Workflows

• BcdiPipeline User Guide
• Beamline-Specific Guide
• Coordinate Systems and Transformations
  • Overview of Coordinate Systems
  • Geometry Class
  • SpaceConverter Class
  • Practical Examples
  • Common Pitfalls
  • Advanced Topics
  • See Also
• Wavefront Analysis and Probe Characterisation
  • Overview
  • Basic Probe Metrics
  • Wavefront Propagation
  • Finding the Focal Plane
  • Visualising Propagated Probe
  • Practical Examples
  • Common Pitfalls
  • References
  • See Also

Advanced Topics

• Detector Geometry Calibration
  • Why Calibration Matters
  • Calibration Parameters
  • Obtaining Calibration Parameters
  • Using Calibration in CDIutils
  • Validating Calibration Quality
  • Advanced: Refining Calibration from Data
  • Common Pitfalls
  • See Also
• Phase Retrieval Parameter Tuning
• Reciprocal Space Gridding
• Strain Analysis
• Facet Analysis

Reference

• Troubleshooting
• Performance Tips
• Data Formats

Overview

This user guide is organized by workflow:

For typical users:

BcdiPipeline User Guide covers the automated BcdiPipeline

For beamline scientists:

Beamline-Specific Guide explains beamline-specific configurations

For manual processing:

Coordinate Systems and Transformations shows how to use converters directly

For optimizing results:

Phase Retrieval Parameter Tuning and Detector Geometry Calibration

Quick Links by Task

“How do I…”

• Load data from my beamline? → Beamline-Specific Guide

• Set up detector calibration? → Detector Geometry Calibration

• Improve phase retrieval quality? → Phase Retrieval Parameter Tuning

• Handle coordinate transformations? → Coordinate Systems and Transformations

• Analyse the reconstructed probe? → Wavefront Analysis and Probe Characterisation

• Calculate strain correctly? → Strain Analysis

• Find crystallographic facets? → Facet Analysis

• Reduce memory usage? → Performance Tips

• Debug failed reconstructions? → Troubleshooting