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 # Try 2: change resolution from 1.8 to 3.0 �~E. # Try 2: change resolution from 3.0 to 2.0 �~E. 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:
- 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: