Section 11.3.3.1. Spot extraction

The region around a spot is defined by the two parameters and , which represent spot diameter and reflecting range, respectively. It is assumed that the coordinates of all image pixels contributing to the intensity of a spot satisfy and when mapped to the profile coordinate system defined in Section 11.3.2.3. Regions of neighbouring reflections may overlap. As implemented in XDS, potential overlap is dealt with by a simple strategy: pixels within the overlap region are assigned to the nearest spot. This is carried out in two steps. First, reflections predicted to occur on a given rotation image are found by generating and testing all possible indices h, k, l up to the highest resolution recorded by the detector. Reflection indices, coordinates of the diffracted beam wave vector and the expected fraction of spot intensity recorded on the image are saved in a table. In the second step, each reflection boundary is traced in the image and corrected to exclude pixels belonging to overlapping reflections, which are rapidly located in the table by the hash technique. The image scaling factor obtained from the mean image background and the neighbourhood pixel values belonging to the reflections recorded in the image are saved on a scratch file dedicated to the currently processed data image.

At regular intervals, these files are merged such that all pixel values belonging to a spot found in the contributing images follow each other. Reflections for which contributing pixels are expected further ahead in data processing are just copied to a scratch output file. The other reflections are mapped to the Ewald sphere, as described below, and their three-dimensional profiles and accompanying information are routed to the main output file of the spot-extraction step. After the file-merging procedure, spot extraction continues.