dials.slice_sequence

Introduction

Slice a sequence to produce a smaller sequence within the bounds of the original. If experiments are provided, modify the scan objects within this. If reflections are provided, remove reflections outside the provided image ranges. Each image_range parameter refers to a single experiment ID, counting up from zero. Any reflections with experiment ID not matched by a image_range parameter are removed.

Examples:

dials.slice_sequence models.expt observations.refl "image_range=1 20"

dials.slice_sequence models.expt "image_range=1 20"

# Two experiments and reflections with IDs '0' and '1'
dials.slice_sequence models.expt observations.refl     "image_range=1 20" "image_range=5 30"

Basic parameters

output {
  reflections_filename = None
  experiments_filename = None
}
image_range = None
block_size = None

Full parameter definitions

output {
  reflections_filename = None
    .help = "The filename for output reflections sliced to remove those"
            "outside the reduced image range. By default generated"
            "automatically from the input name"
    .type = str
  experiments_filename = None
    .help = "The filename for the output experiments with sliced scans.
      "
            "        By default generated automatically from the input name"
    .type = str
}
image_range = None
  .help = "Range in images to slice a sequence. The number of arguments must"
          "be a factor of two. Each pair of arguments gives a range that"
          "follows C conventions (e.g. j0 <= j < j1) when slicing the"
          "reflections by observed centroid."
  .type = ints(size=2)
  .multiple = True
block_size = None
  .help = "Overrides image_range if present. This option splits each sequence"
          "into the nearest integer number of equal size blocks close to"
          "block_size degrees in width"
  .type = float(allow_none=True)
exclude_images_multiple = None
  .help = "Overrides image_range and block_size if present. This option splits"
          "each scan at the specified image and at each multiple of this image"
          "number in each experiment. The specified images are also excluded"
          "from the resulting scans. This is provided as an alternative method"
          "for specifying image exclusions for cRED data, where the scan of"
          "diffraction images is interrupted at regular intervals by a crystal"
          "positioning image (typically every 20th image). The alternative is"
          "using the same-named parameter in dials.integrate, where it acts as"
          "a mask for images while keeping a single scan. Splitting the scan"
          "may be more appropriate if the experimental geometry changes after"
          "collecting calibration images."
  .type = int(allow_none=True)
  .expert_level = 2