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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

# Open the HDF5 file containing detector data
h5name = "scan-1737_pilatus.h5"
h = h5py.File(h5name, 'r')
# Read an image frame from the dataset
img = h['/entry/instrument/pilatus/data'][10]
# Specify the PONI file (detector geometry calibration)
poni = 'Si_135mm.poni'
# Create a mask with the same shape as the image
mask = 'hot_px_bs_mask.npy'


# Configuration for the azimuthal integration
config = {
    'poni': poni,                      # Path to the PONI file
    'mask': mask,                      # Mask to ignore bad pixels
    'radial_bins': 3000,               # Number of radial bins for integration
    'azimuth_bins': 180, # or None     # Number of azimuthal bins (for 2D integration)
    'n_splitting': 21,                 # Number of subdivisions per pixel (for precision)
    'error_model': 'poisson',          # Error propagation model
    'solid_angle': True,               # Apply solid angle correction
    'polarization_factor': 0.965,      # Correction for polarization effects
    'normalized': True,                # Normalize the output intensities
    'unit': '2th',   # or q            # Output units (e.g., 2θ, q)
}
# Create the azimuthal integrator instance using azint
ai = azint.AzimuthalIntegrator(**config)
# Perform the azimuthal integration on the image
data = ai.integrate(img)


# Configuration for the NXWriter (NeXus HDF5 file writer)
init_writer_config = {
    'ai': ai,                                   # AzimuthalIntegrator instance
    'output_file': 'nx_azint1d_azint2d.h5',     # Output file name
    'write_1d': True,                           # Whether to write 1D integration data
    'write_2d': True,                           # Whether to write 2D (cake) integration data (False if azimuth_bins is None)
    'instrument_name': 'DanMAX',                # Name of the beamline or instrument
    'source_name': 'MAX IV',                    # Name of the facility or source
    'source_type': 'Synchrotron X-ray Source',  # Type of source
    'source_probe': 'X-ray',                    # Type of probe used (e.g., x-ray, neutron)
}
# Create the NXWriter instance and write the data to the file
nx = azint_writer.NXWriter(**init_writer_config)
# Add the integrated data to the file
nx.add_data(data)

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.