Difference between revisions of "Phil"

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Several lines of parameters are given, then a few parameter blocks are specified, enclosed in {} brackets.  The parameters in detail:
 
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).
 
* 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.  Must be in the primitive setting as currently implemented.  Therefore, if the cell is centered, convert the dimensions to the primitive setting with "iotbx.lattice_symmetry".
+
* target_cell: known unit cell for this sample.  In the form a, b, c, alpha, beta, gamma.  Must be in the primitive setting as currently implemented.  Therefore, if the cell is centered, convert the dimensions to the primitive setting with ''iotbx.lattice_symmetry''.
 
* known_setting: < Nick will add a description and how to derive this soon >
 
* 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.   
 
* distl_highres_limit and force_method2_resolution_limit: only process to this resolution limit.   

Revision as of 02:36, 4 October 2013

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. Must be in the primitive setting as currently implemented. Therefore, if the cell is centered, convert the dimensions to the primitive setting with iotbx.lattice_symmetry.
  • 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)