Phil

As described in the overview, phil files contain parameters used during hitfinding, indexing and integration. This tutorial uses two phil files during the indexing and integration step: Ls04-lysozyme.phil and metrology-7.1.phil. The former specifies parameters specific to the processing run, while the latter specifies whole-pixel and sub-pixel metrology corrections applied to the 64 CSPAD sensor tiles.

Hitfinding/indexing/integration phil file

For the tutorial, Ls04-lysozyme.phil, stored in the /reg/d/ffb/cxi/temp/cctbx/tutorials/indexing directory but copied to your ~/myrelease directory during use, contains configuration settings we worked out that best process this data. The file will look like this:

# -*- mode: Conf -*-

include file metrology-7.1.phil

# From looking at 35 images integrated with detz_offset = 581 and
# without target_cell set.
target_cell = 38 79 79 90 90 90
known_setting = 9

distl_highres_limit = 2.0
force_method2_resolution_limit = 2.0

mosaicity_limit = 1

# Set to True to pick up second lattice, if present.
#outlier_detection_switch = True

# TEST
distl_minimum_number_spots_for_indexing = 20

distl {
  res.outer = 2.0
  minimum_signal_height = 5
  #minimum_spot_height = 10
  minimum_spot_height = 5
  minimum_spot_area = 1
  spot_area_maximum_factor = 20
  compactness_filter = False
  #method2_cutoff_percentage = 5
  method2_cutoff_percentage = 2.5

  # Avoids intensity filter.
  #peak_intensity_maximum_factor = 10000
  peak_intensity_maximum_factor = 100
}

indexing {
  # Set to True to generate correction vectors.
  verbose_cv = True
}

integration {
  background_factor = 2

  #detector_gain = 7.5
  detector_gain = 1.0

  #model = use_case_3_simulated_annealing_7
  model = user_supplied

  signal_penetration = 0.5
  #spot_shape_verbose = True
  spotfinder_subset = spots_non-ice
}

Several lines of parameters are given, then a few parameter blocks are specified, enclosed in {} brackets. The parameters in detail:

• include file metrology-7.1.phil: this line specifies another phil file to include. In this case, the included file specifies metrology corrections (see below).
• target_cell: known unit cell for this sample. In the form a, b, c, alpha, beta, gamma
• known_setting: < Nick will add a description and how to derive this soon >
• distl_highres_limit and force_method2_resolution_limit: only process to this resolution limit.
• mosaicity_limit: maximum moisicity before a frame is rejected
• distl_minimum_number_spots_for_indexing: indexing will not proceed unless there are at least this many good spots found on the image
• Subcategory distl: parameters specific to spot finding
  • res.outer: resolution limit for spotfinder
  • minimum_signal_height: in units of background noise sigma, how much signal is needed for a spot
  • minimum_spot_height: minimum height for a pixel to be considered a maximum (after it's determined to be signal)
  • minimum_spot_area: minimum area in pixels for each spot
  • spot_area_maximum_factor: in multiples of minimum spot area, how large spots are allowed to be
  • compactness_filter: < Nick to add a description here >
  • method2_cutoff_percentage: < Nick to add a description here >
  • peak_intensity_maximum_factor: a peak intensity filter
• Subcategory indexing:
  • verbose_cv: if true, correction vectors are generated < more detail here >
• Subcategory: integration
  • background_factor:
  • detector_gain: ADU units per photon
  • model: labelit has several integration models, and allows users to provide their own. The model listed here is custom for these xfel applications
  • signal_penetration: thickness of the CSPAD sensors.
  • spotfinder_subset: which spots found by spotfinder to use. Choose from: < add >

Metrology phil

cctbx.xfel applies 4 levels of metrology:

• Optical metrology: this is supplied by LCLS. The pyana config file specifies a path to a directory where initial tile placements are specified.
• Quadrant translations: adjustments to each of the 4 quadrants as a whole.
• Unit-pixel or whole-pixel metrology: a series of whole-pixel translations applied to each tile.
• Sub-pixel metrology: fractional corrections including translations and rotations of each tile. Used during integration.

The latter two corrections are contained in the metrology phil file. For this tutorial that is metrology-7.1.phil:

distl {
  detector_format_version = "CXI 7.1"
  detector_tiling = None
  peripheral_margin = 1

  quad_translations =  2 -6  3 -6 -7  0 -1 -4
  tile_translations =  2  1  1  1  1  2  0  2  3  0  0  0  4  1  3  1 \
  ...
)
integration {
  # This is L785_119.
  subpixel_joint_model {
    rotations = \
       0.1056719175    0.1080664532  -0.2151669703  -0.2099097279   \
       ...
    translations = \
       0.2700895641   -0.6117579705  -0.5111648376  -0.8676594815   \
       ...
  }
}

These parameters are in detail:

• distl subsection: quadrant translations and single-pixel tile translations
  • detector_format_version: deprecated.
  • detector_tiling: < add >
  • peripheral_margin: how many pixels to leave as a border around the final image
  • quad_translations: set of x/y adjustmants to each quadrant
  • tile_translations: set of x/y adjustments to each tile (128 total)
• integration subsection: sub-pixel adjustments applied during reflection integration:
  • subpixel_joint_model: root tag for the sub-pixel corrections
    • rotations: angles in degrees for each tile (64)
    • translation: x/y translations for each tile (128)