NeuNorm 2.2.2

Neutron imaging normalization and TOF data processing for ORNL facilities

NeuNorm 2.0 - Modern Neutron Imaging Normalization

NeuNorm normalizes neutron imaging data and processes time-of-flight (TOF) data for ORNL imaging facilities — MARS at HFIR and VENUS at SNS.

NeuNorm 2.0 is a complete, scipp-based rewrite and a breaking change from the 1.x series. Code written against the 1.x NeuNorm.normalization.Normalization API will not run unchanged on 2.0. See the 1.x → 2.0 migration guide to port your code, or pin NeuNorm<2 to keep using the legacy API — see NeuNorm 1.x (Legacy).

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Overview

NeuNorm 2.0 is a ground-up rewrite for modern neutron imaging workflows at ORNL facilities:

Facility	Beamline	Beam Type	Detectors
HFIR	MARS	Continuous	CCD/CMOS, TPX3
SNS	VENUS	Pulsed (TOF)	CCD/CMOS, TPX1, TPX3

Key Features

• Time-of-Flight (TOF) Support: Full hyperspectral data processing
• Event-Mode Processing: Direct TPX3 event handling with pulse reconstruction
• Automatic Uncertainty Propagation: Via scipp's variance tracking
• Dual-Facility Support: Unified API for MARS and VENUS workflows
• Modern Architecture: Pydantic v2 data models, scipp-based processing

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Installation

From PyPI:

pip install NeuNorm
# optional extras: visualization (plopp/matplotlib) and Numba acceleration
pip install "NeuNorm[viz,performance]"

From conda (the neutronimaging channel):

conda install neutronimaging::neunorm

From source, for development (uses pixi):

git clone https://github.com/ornlneutronimaging/NeuNorm.git
cd NeuNorm
pixi install
pixi run test

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Quick Start

Each detector/facility combination has a ready-made pipeline in neunorm.pipelines that loads the data, applies the appropriate corrections, and writes the normalized transmission — with uncertainty, detector masks, and provenance metadata — to HDF5 (or TIFF):

from pathlib import Path
from neunorm.pipelines.mars_ccd import run_mars_ccd_pipeline

# Each inner list is one acquisition "run" to combine before processing.
transmission = run_mars_ccd_pipeline(
    sample_paths=[["sample_0001.tiff", "sample_0002.tiff"]],
    ob_paths=[["ob_0001.tiff", "ob_0002.tiff"]],
    dark_paths=[["dark_0001.tiff"]],  # optional — omit to skip dark correction
    output_path=Path("normalized.hdf5"),
)

Each detector/facility has its own pipeline — run_mars_tpx3_pipeline, run_venus_ccd_pipeline, run_venus_tpx1_pipeline, run_venus_tpx3_histogram_pipeline, and run_venus_tpx3_event_pipeline. They share the same load → correct → normalize → write-to-HDF5/TIFF flow, but each takes detector-appropriate inputs — dark_paths is optional for the CCD pipelines (omit it to skip dark correction) and TPX detectors skip it entirely, the TOF pipelines add rebin_by_tof/rebin_by_spatial, and run_venus_tpx3_event_pipeline takes a BinningConfig and flat (per-run) path lists. Check each function's signature in the API reference or the per-workflow guides under Supported Workflows. Verify your install with:

python -c "import neunorm; print(neunorm.__version__)"

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Core Physics

Normalization Principle

Neutron imaging normalization removes detector noise, beam fluctuations, and contamination to extract the true sample transmission:

$$ T(x, y) = f_{beam} \times \frac{I_{sample} - I_{dark}}{I_{OB} - I_{dark}} $$

Where:

• T: Transmission (0-1, may exceed 1 due to scattering)
• I_sample: Raw sample measurement (counts)
• I_OB: Open beam reference (no sample)
• I_dark: Dark current (detector noise baseline)
• f_beam: Beam intensity correction factor

Detector-Specific Corrections

Detector Type	Dark Correction	Beam Correction	Hot Pixels
CCD/CMOS	Optional	Time or p_charge	Not needed
TPX1 (histogram)	Not needed	p_charge or shutter	Not needed
TPX3 (event/histogram)	Not needed	p_charge (VENUS); none (MARS)	Required

Uncertainty Propagation

For counting detectors, uncertainty follows Poisson statistics:

$$ \frac{\sigma_T}{T} = \sqrt{\frac{1}{N_{sample}} + \frac{1}{N_{OB}} + \left(\frac{\sigma_{p,sample}}{p_{sample}}\right)^2 + \left(\frac{\sigma_{p,OB}}{p_{OB}}\right)^2} $$

For CCD/CMOS with dark correction, additional terms account for dark current uncertainty.

Time-of-Flight (TOF) Processing

At VENUS (pulsed source), neutron wavelength is determined from flight time:

$$ \lambda = \frac{h \times t}{m_n \times L} $$

Where:

• λ = neutron wavelength
• t = time-of-flight
• L = source-to-detector distance
• m_n = neutron mass
• h = Planck's constant

This enables hyperspectral imaging with wavelength-resolved transmission T(λ, x, y).

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Supported Workflows

Workflow	Detector	Facility	TOF	Documentation
MARS CCD/CMOS	CCD/CMOS	HFIR	No	mars_ccd_cmos.md
MARS TPX3	Timepix3	HFIR	No	mars_tpx3.md
VENUS CCD/CMOS	CCD/CMOS	SNS	No	venus_ccd_cmos.md
VENUS TPX1	Timepix1	SNS	Yes	venus_tpx1.md
VENUS TPX3	Timepix3	SNS	Yes	venus_tpx3.md

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Architecture

Technology Stack

• Data Models: Pydantic v2 for validation
• Array Processing: scipp with automatic variance propagation
• TIFF I/O: Pillow (input), scitiff (output)
• Performance: Numba JIT for hot paths (optional, via the performance extra)
• Testing: pytest with coverage

Key Design Principles

1. Scipp-native: All processing uses sc.DataArray with automatic uncertainty tracking
2. Modular pipelines: Each processing step is an independent, testable module
3. Workflow-driven: Pipelines are composed based on detector/facility combination
4. Explicit over implicit: Configuration via Pydantic models, no hidden defaults

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Documentation

Full documentation — user guides plus an autodoc API reference — is hosted at neunorm.readthedocs.io. The per-workflow guides live under docs/workflows/. Release history is in CHANGELOG.md, and the 1.x → 2.0 migration guide covers porting legacy code.

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Contributing

See CONTRIBUTING.md. Development uses pixi; please run pixi run test and pixi run pre-commit run --all-files before opening a pull request. Branches follow the promotion path next → qa → main (next is the default development branch).

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NeuNorm 1.x (Legacy)

NeuNorm 1.x — the from NeuNorm.normalization import Normalization API — is the previous stable line. To keep using it, pin NeuNorm<2 in your environment. Archived 1.x documentation: archive/neunorm-1.x/README.md. To port existing 1.x code to 2.0, see the migration guide.

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References

• scipp documentation
• scitiff documentation
• ORNL Neutron Imaging

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Acknowledgements

This work is sponsored by the Laboratory Directed Research and Development Program of Oak Ridge National Laboratory, managed by UT-Battelle LLC, under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy.

License

BSD 3-Clause License. See LICENSE for details.

Citation

If you use NeuNorm in your research, please cite:

@article{bilheux2018neunorm,
  title={NeuNorm: Open-source normalization of neutron imaging data in Python},
  author={Bilheux, Jean-Christophe},
  journal={Journal of Open Source Software},
  volume={3},
  number={28},
  pages={815},
  year={2018},
  doi={10.21105/joss.00815}
}