extract_intensities_summation_method#
- IntegrationGenerator.extract_intensities_summation_method(box_inner: int = 7, box_outer: int = 10, n_min: int = 5, n_max: int = 1000, snr_thresh: float = 3.0)[source]#
Integrate reflections using the summation method. Two boxes are defined, the inner box is used to define the integration area. The outer box is used to calculate the average signal-to-noise ratio (SNR). All pixels with a large enough SNR are considered to be signal. The largest region of connected signal pixels are summed to calculate the reflection intensity. The diffraction vectors are calculated as the center of mass of the signal pixels.
- Parameters:
box_inner (int) – Defines the size of the inner box, which must be larger than the reflection.
box_outer (int) – Defines the size of the outer box. The border between the inner and outer box is considered background and used to calculate the (SNR) for each pixel: SNR = (I - <I>/std(I_bkg)).
snr_thresh (float) – Minimum signal-to-noise for a pixel to be considered as signal.
n_min (int) – If the number of SNR pixels in the inner box < n_min, the reflection is discared
n_max – If the number of SNR pixels in the inner box > n_max, the reflection is discareded
verbose (bool) – Print statistics for every reflection (for debugging)
- Returns:
vectors – DiffractionVectors with optimized coordinates, where the attributes vectors.intensities -> I, vectors.sigma -> sigma(I), and vectors.snr -> I / sigma(I)
- Return type:
Notes
- Implementation based on Barty et al, J. Appl. Cryst. (2014). 47, 1118-1131
Lesli, Acta Cryst. (2006). D62, 48-57