NeXus azint writer

azint-writer is a Python package for writing HDF5 files in the NXazint1d or NXazint2d format, a new extension to the NeXus standard. The NXazint1d (NXazint2d) format is specifically designed for storing data related to azimuthal integration in diffraction experiments.

Note: The azint-writer package is currently coupled to the azint library for performing azimuthal integration.

Features

• HDF5 File Writing: Easily generate NeXus-compliant HDF5 files.
• azint-writer Format: Supports the new azint-writer format for azimuthal integration.
• Customizable Configuration: Flexible options for writing metadata and experimental data.
• Seamless Integration: Compatible with existing NeXus tools and libraries.

Installation

Install azint-writer via conda:

conda install -c maxiv azint-writer

azint-writer Format

• Experiment Metadata: Beamline details, sample information, and experimental setup.
• Azimuthal Integration Data: One-dimensional and two-dimensional (cake) integration results.
• Calibration Information: Detector geometry and calibration parameters.

For more information about the NeXus standard, see the official documentation.

Example Usage

Here is a sample Python snippet using azint-writer: (link to file examples and output)

import azint, azint_writer, h5py
import numpy as np

# ------------------------------
# Load detector image and setup
# ------------------------------

# Path to the input HDF5 file containing detector data
h5name = "scan-1737_pilatus.h5"
h = h5py.File(h5name, 'r')

# Extract a single image frame from the dataset
img = h['/entry/instrument/pilatus/data'][10]

# Path to the detector calibration file
poni = 'Si_135mm.poni'

# Path to the mask file for bad pixels or beamstop
mask = 'hot_px_bs_mask.npy'

# ------------------------------
# Azimuthal integration settings
# ------------------------------

config = {
    'poni': poni,                      # Detector geometry calibration file
    'mask': mask,                      # Mask to ignore hot/dead pixels
    'radial_bins': 3000,              # Number of radial bins
    'azimuth_bins': 180,              # Number of azimuthal bins (set to None for 1D only)
    'n_splitting': 21,                # Pixel subdivision for integration precision
    'error_model': 'poisson',         # Error model for propagation
    'solid_angle': True,              # Apply solid angle correction
    'polarization_factor': 0.965,     # Correction for polarization effects
    'normalized': True,               # Normalize intensity values
    'unit': '2th',                    # Output units (e.g., '2th' for 2θ)
}

# ------------------------------
# Output file and metadata config
# ------------------------------

# Create the azimuthal integrator instance
ai = azint.AzimuthalIntegrator(**config)

# Configuration for writing NeXus-compliant HDF5 output
init_writer_config = {
    'ai': ai,
    'output_file': 'nx_azint1d_azint2d.h5',
    'write_1d': True,
    'write_2d': True,  # Set to False if azimuth_bins is None
    'instrument_name': 'DanMAX',
    'source_name': 'MAX IV',
    'source_type': 'Synchrotron X-ray Source',
    'source_probe': 'X-ray',
}

# Create writer instance
nx = azint_writer.NXWriter(**init_writer_config)

# ------------------------------
# Perform integration and save
# ------------------------------

# Integrate the selected image
data = ai.integrate(img) # data = (I, errors_1d, I_2d, errors_2d)

# Add the integrated data to the NeXus HDF5 file
nx.add_data(data)

# ------------------------------
# Optionally add monitor data
# ------------------------------
from azint_writer import add_monitor

# A 1D array of monitor counts per image (must match number of images)
monitor = [1, ..., nImg]  # Replace with actual monitor data
add_monitor("nx_azint1d_azint2d.h5", monitor)

Contributing

We welcome and encourage contributions to azint-writer! Here's how you can get involved:

• Fork the repository.
• Create a new branch for your feature or bug fix.
• Submit a pull request with a clear and concise description of your changes.

Please make sure your contributions follow the NeXus standard guidelines, especially when adding features related to azint-writer.

License

This project is licensed under the MIT License. See the LICENSE file on GitHub for details.

Support

If you encounter any issues, have questions, or would like to suggest improvements, feel free to open an issue on the project’s GitHub issue tracker.