pyreflect-nr 1.4.5

The package tool for neutron reflectivity analysis

NR-SCFT-ML: Neutron Reflectivity SCFT Machine Learning

A Python package for Neutron Reflectivity data analysis using Machine Learning.
Including Chi parameter prediction from SLD profile data and SLD profile prediction from NR curves.

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Overview

NR-SCFT-ML (implemented as the pyreflect package) is a Python toolkit for efficient processing and analysis of Neutron Reflectivity (NR) data. It provides a streamlined pipeline for:

• Preprocessing NR datasets
• Predicting SLD profiles using CNN-based models
• Predicting Chi parameters using a combined Autoencoder and MLP architecture

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Prerequisites

• Python >= 3.10
• Strongly recommended: Conda (local machines and HPC clusters)
• Optional: GPU with CUDA-capable PyTorch build for faster training and inference

Large-scale synthetic data generation and model training are memory intensive. HPC resources or a workstation with large RAM and optionally a GPU are recommended.

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Installation

pyreflect depends on scientific Python libraries with native extensions (NumPy, SciPy, refnx, refl1d, etc.).
For reliability across platforms, Conda is the recommended installation method, especially on Windows and HPC systems.

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Option 1. ✅ Recommended: Conda (Local or HPC)

1. Create and activate a Conda environment

conda create -n pyreflect python=3.10
conda activate pyreflect

2. Install scientific dependencies via conda-forge

conda install -c conda-forge \
    numpy scipy refnx refl1d numba llvmlite

3. Install pyreflect

pip install pyreflect-nr

After installation, you can access the CLI via:

python -m pyreflect --help

GPU support (optional)

For GPU-accelerated training and inference, install a CUDA-enabled PyTorch build inside the same environment, following the official PyTorch instructions for your system or cluster.

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Option 2. 🛠 Automated setup (using setup.sh)

This repository provides a helper script setup.sh that:

• Detects your Conda installation
• Creates a Conda environment named pyreflect (Python 3.10)
• Installs core scientific dependencies
• Registers a Jupyter kernel called Python (pyreflect)

You can fetch and run it as follows:

curl -fsSLo setup.sh https://raw.githubusercontent.com/williamQyq/pyreflect/main/setup.sh
bash setup.sh

After it completes:

• In Jupyter, select the Python (pyreflect) kernel
• The environment is ready for use

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⚠️ pip-only installation (not recommended on Windows)

A pure pip installation may work on Linux or macOS systems with a full build toolchain.
On Windows, this may require Microsoft C++ Build Tools and is not recommended.

python -m venv .venv
source .venv/bin/activate  # Windows: .venv\Scripts\activate
pip install --upgrade pip
pip install pyreflect-nr

If installation fails due to native extensions, switch to the Conda workflow above.

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👩‍💻 Development setup (for contributors)

Poetry is used for development and maintenance, not for end-user installation.

git clone https://github.com/williamQyq/pyreflect.git
cd pyreflect

poetry install
poetry shell

You can then run:

python -m pyreflect --help

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Example Notebooks

Example notebooks are available in the examples directory:

• examples/example_reflectivity_pipeline.ipynb – end-to-end NR → SLD pipeline for Experimental Data
• examples/example_reflectivity_pipeline.ipynb – end-to-end NR → SLD pipeline for Simulated Data
• examples/example_notebook_generate_training_datasets.ipynb – synthetic NR/SLD dataset generation
• examples/example_notebook_autoencoder.ipynb – Autoencoder + MLP workflow for Chi prediction
• examples/example_notebook_PCA_NR_check.ipynb – NR data exploration and PCA

Tutorial video:

For detailed CLI usage, configuration, and typical research workflows, see docs/usage.md.

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Credits

This project builds on work by:

• Brian Qu (NR-SLD-CNN)
• Dr. Rajeev Kumar
• Prof. Miguel Fuentes-Cabrera (NR-SCFT-ML)
• Shanshou Li
• Hudson Kass
• Francisco Jimenez

Author

Yuqing Qiao (William) – Maintainer and developer
Shanshou Li - Developer
Hudson Kass - Developer Francisco Jimenez - Validator