laue-analysis

A Python package and collection of C binaries for Laue diffraction data analysis at beamline 34IDE, including indexing and wire scan reconstruction capabilities.

Package Structure

src/
└── laueanalysis/
    ├── indexing/                   # Laue indexing submodule
    │   ├── pyLaueGo.py            # Main orchestrator for data processing
    │   ├── mpi_runner.py          # MPI-based execution utilities
    │   ├── xmlWriter.py           # XML output writer
    │   ├── lau_dataclasses/       # Data models (atom, detector, HKL, pattern, etc.)
    │   ├── bin/                   # Compiled C executables (euler, peaksearch, pix2qs)
    │   └── src/                   # C source trees (euler, peaksearch, pixels2qs)
    ├── reconstruct/               # Wire scan reconstruction submodule
    │   ├── wirescan_interface.py  # Python interface for reconstruction C program
    │   ├── bin/                   # Compiled C executable (reconstructN_cpu)
    │   └── source/                # C source code for reconstruction
    │       └── recon_cpu/         # CPU-based reconstruction implementation
    └── __init__.py

• Indexing C binaries (euler, peaksearch, pix2qs) live under src/laueanalysis/indexing/bin/ after installation.
• Reconstruction C binary (reconstructN_cpu) lives under src/laueanalysis/reconstruct/bin/ after installation.
• Source under src/laueanalysis/*/src/ is included for reference; users do not invoke it directly.

Installation

Prerequisites:

• Python ≥ 3.12
• System libraries and tools: [make, gcc, h5cc], GNU Scientific Library (GSL), HDF5 development libraries
• Python dependencies: numpy, pyyaml, h5py, mpi4py
• NOTE: The conda packaging is compatible only with linux. Many of the underlying dependencies aren't available for other system.

Install from source:

git clone https://github.com/yourusername/laue_indexing.git
cd laue_indexing
python3 -m pip install .

The setup.py build step will compile the C binaries into both src/laueanalysis/indexing/bin/ and src/laueanalysis/reconstruct/bin/.

Configuration

Provide a YAML config file (see tests/data/test_config.yaml for an example). Key entries:

• filefolder: Directory of input HDF5 files
• geoFile: Path to the geometry XML file
• crystFile: Path to the crystal-structure file
• outputFolder: Directory for generated output
• Optional range filters: scanPointStart, scanPointEnd, depthRangeStart, depthRangeEnd

Usage

Laue Indexing

Command-line / MPI

Run with MPI to parallelize:

mpirun -np 32 python -m laueanalysis.indexing.pyLaueGo path/to/config.yml

Python API

import yaml
from laueanalysis.indexing.pyLaueGo import PyLaueGo

with open('path/to/config.yml') as f:
    config = yaml.safe_load(f)

processor = PyLaueGo(config=config)
processor.run_on_process()  # single-process execution

Wire Scan Reconstruction

The reconstruction module provides a Python interface to the reconstructN_cpu C program for depth-resolved wire scan analysis. See the test files for usage examples.

Output Layout

Indexing Results

Results are written under outputFolder as:

input_basename.xml          # Final processed XML
error_TIMESTAMP.log         # Error log
index/index_out_0_0.txt     # Index subprocess outputs
p2q/p2q_out_0_0.txt         # Pixels→Q space outputs
peaks/peaks_out_0_0.txt     # Peak-search outputs

Reconstruction Results

Wire scan reconstruction outputs depth-resolved image files:

recon_prefix_depth_XXX.h5   # Reconstructed depth slices
recon_prefix_metadata.xml   # Reconstruction metadata

Testing

Run the full test suite:

python -m pytest tests/ -v