# -*- mode: python; coding: utf-8; indent-tabs-mode: nil; python-indent: 2 -*- from __future__ import absolute_import, division, print_function #Phil parameters required to process data from Stanford LCLS CXI instrument def cxi_basic_start(): try: from labelit import preferences from rstbx.command_line.index import special_defaults_for_new_horizons except Exception: # option to view images or open pickle files without any LABELIT dependency from rstbx.phil import preferences def special_defaults_for_new_horizons(phil_scope): # for integration, do not want 2x2 binning phil_scope.merge_command_line(["distl_permit_binning=False"]) new_horizons_phil = preferences.RunTimePreferences() special_defaults_for_new_horizons( new_horizons_phil ) common_arguments = [ "distl.bins.verbose=True", "distl.minimum_spot_area=3", "distl.peripheral_margin=1", "distl.peak_intensity_maximum_factor=10000.", #avoids intensity filter "distl.compactness_filter=True", ] new_horizons_phil.merge_command_line(common_arguments) return new_horizons_phil def cxi_versioned_extract(*args): import copy # args is one or more lists of phil parameters, as would be passed # in through the command line; to be processed sequentially. working_phil = cxi_basic_start() #for arg in args: for arg in copy.deepcopy(args): working_phil.merge_command_line(arg) working_extract = working_phil.command_extractor if working_extract.distl.tile_translations is not None and \ working_extract.distl.quad_translations is not None: return working_extract # Get the working tile translations for the given detector format version # from previous experiments legacy_extract = cxi_versioned_extract_detail(args) if working_extract.distl.tile_translations is None: working_extract.distl.tile_translations = legacy_extract.distl.tile_translations if working_extract.distl.quad_translations is None: working_extract.distl.quad_translations = legacy_extract.distl.quad_translations return working_extract def cxi_versioned_extract_detail(args): # args is one or more lists of phil parameters, as would be passed # in through the command line; to be processed sequentially. working_phil = cxi_basic_start() for arg in args: working_phil.merge_command_line(arg) #distl_args = [a.object.as_str().strip() for a in working_phil.phil_scope.all_definitions()] cxi_version = working_phil.phil_scope.get("distl.detector_format_version" ).extract().detector_format_version print("cxi_versioned_extract()::cxi_version:", cxi_version) if cxi_version in ["CXI 3.1","CXI 3.2"]: working_extract = working_phil.command_extractor # Three sensors were disabled at this time. The 2D-translations # will have (32 - 3) * 2 * 2 = 116 components. corrected_auxiliary_translations = [ 1, 1, 1, 1, 1, 2, 1, 2, 0, 0, 0, 0, 1, -1, 1, -1, 1, -2, 1, -2, 0, -2, 0, -2, -1, 1, -1, 1, 1, 0, 1, 0, 2, -1, 2, -1, -3, 1, -3, 1, -4, 0, -4, 0, 4, 0, 4, 0, -7, 4, -7, 4, 2, -1, 2, -1, 1, -2, 1, -2, -1, 1, -1, 1, -1, 1, -1, 1, 0, -1, 0, -1, 2, -2, 2, -2, 0, 1, 0, 1, 0, 2, 0, 2, -1, -2, -1, -2, -1, -3, -1, -3, 1, 1, 1, 1, 0, 1, 0, 1, 0, -1, 0, -1, 1, -2, 1, -2, -2, -1, -2, -1, 2, 2, 2, 2] from scitbx.array_family import flex total_tile_translations = flex.int(corrected_auxiliary_translations) TT = list(total_tile_translations) working_extract.distl.tile_translations = TT working_extract.distl.quad_translations = [-19, 15, 21, 14, -25, -20, 20, -15] return working_extract elif cxi_version in ["CXI 4.1"]: working_extract = working_phil.command_extractor corrected_auxiliary_translations = [ 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,-1,0,-1, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,-2, 0,0,0,-1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0,0,0] from scitbx.array_family import flex total_tile_translations = flex.int(corrected_auxiliary_translations) TT = list(total_tile_translations) working_extract.distl.tile_translations = TT #working_extract.distl.quad_translations = [0,0,0,0,0,0,0,0] #working_extract.distl.quad_translations = [5,-5,6,-9,-5,-2,0,-8] working_extract.distl.quad_translations = [6,-2,7,-4,-4,1,1,-5] return working_extract elif cxi_version in ["CXI 5.1"]: working_extract = working_phil.command_extractor # The auxiliary translations are modified with respect to CXI 4.1. If the # SLAC-provided metrology were to be trusted, this would be be all # zeros? corrected_auxiliary_translations = [ 1,-1,1,0,0,-1,0,-1,2,0,0,0,3,1,2,0,2,-1,2,-1, 0,0,1,0,1,-2,1,-3,0,-1,0,-1,-2,1,0,1,-1,0,0,0, 0,2,-1,1,0,2,-1,2,0,0,0,0,0,0,1,1,1,0,0,0, -1,0,-1,0,1,1,0,0,0,1,0,1,0,-1,0,0,1,-2,0,0, -1,-2,-1,-1,0,0,-1,-1,0,0,0,1,-1,-1,0,0,1,-2,1,-1, 1,-1,0,0,0,-2,0,-3,1,-4,1,-4,-2,0,-1,-1,0,0,-1,-1, -1,1,-1,0,0,1,0,1] from scitbx.array_family import flex total_tile_translations = flex.int(corrected_auxiliary_translations) TT = list(total_tile_translations) #added NKS 8/19/14 #TT = [0]*128 working_extract.distl.tile_translations = TT print("IN CXI %>! WITH ",working_extract.distl.tile_translations) # Order: UL x, UL y, UR x, UR y, LL x, LL y, LR x, LR y working_extract.distl.quad_translations = [-3,-1,-1,-5,-13,2,-7,-4] return working_extract elif cxi_version in ["CXI 6.1"]: working_extract = working_phil.command_extractor corrected_auxiliary_translations = [ 2, 1, 1, 1, 1, 3, -1, 2, 3, 1, 1, 0, 5, 2, 4, 1, 2, -1, 2, 0, 2, 1, 2, 0, -1, -2, -1, -2, -1, 0, -2, 1, -1, 0, 0, 1, 1, 0, 1, 1, -1, 0, -1, 0, -1, 0, -1, 0, 0, 0, -1, 0, 1, 0, 1, 0, 0, 1, 1, 2, -1, 1, 0, 2, -1, 1, 0, 1, 0, 0, 1, 0, -2, 0, -1, 1, -2, -1, -2, 1, -2, 0, -1, 1, -3, -1, -3, 0, 0, 1, 0, 1, 0, 0, 1, 0, 2, 0, 2, -1, 1, 0, 0, -1, 0, 0, 1, -2, 1, -1, 2, -2, -1, 0, 0, -1, -2, 1, 0, 0, -1, 0, -1, -1, 1, 1, 1, -1] from scitbx.array_family import flex total_tile_translations = flex.int(corrected_auxiliary_translations) TT = list(total_tile_translations) working_extract.distl.tile_translations = TT # Order: UL x, UL y, UR x, UR y, LL x, LL y, LR x, LR y working_extract.distl.quad_translations = [0,7,13,8,-8,0,11,-3] return working_extract elif cxi_version in ["CXI 7.1"]: working_extract = working_phil.command_extractor corrected_auxiliary_translations = [ 2, 1, 1, 1, 1, 2, 0, 2, 3, 0, 0, 0, 4, 1, 3, 1, 1, -2, 2, -1, -1, -1, 1, -1, -1, -2, -1, -1, -1, 0, -1, 1, -2, 0, 0, 1, 0, 0, 1, 1, -1, 1, -2, 1, -1, 0, -1, 1, -1, 1, -1, 1, -2, 1, -1, 1, 1, 1, 0, 2, -1, 1, 0, 1, 0, 1, 0, 1, 0, 0, 0, 1, -1, 0, 0, 1, 0, -1, -1, 1, -1, 0, -1, 1, -1, 0, -2, 0, 0, 1, 0, 1, -1, 0, 1, 0, 2, -1, 2, -1, 1, 0, 0, 0, 1, -1, 1, -2, 2, -2, 2, -2, 0, -1, 1, -1, 2, 1, 0, 0, 0, 0, 0, -2, 1, 1, 1, 0] from scitbx.array_family import flex total_tile_translations = flex.int(corrected_auxiliary_translations) TT = list(total_tile_translations) working_extract.distl.tile_translations = TT # Order: UL x, UL y, UR x, UR y, LL x, LL y, LR x, LR y working_extract.distl.quad_translations = [2,-6,3,-6,-7,0,-1,-4] return working_extract elif cxi_version in ["CXI 7.d"]: working_extract = working_phil.command_extractor corrected_auxiliary_translations = [ 1, 1, 1, 0, 0, 0, 0, 0, -2, -1, -1, -1, -1, -3, 0, -3, 2, 3, 2, 1, -1, 4, -1, 2, 0, 1, 1, 1, 0, 2, -1, 2, 0, 0, 0, 0, 0, 0, 0, 0, -3, -2, -3, -1, -2, -1, -2, -1, 3, -3, 3, -3, 5, -2, 4, -2, 2, -1, 2, -1, 2, -2, 2, -1, 1, 1, 1, 0, 0, 0, 0, -1, -1, 2, -2, 2, -2, 0, -1, 0, -1, -2, -1, -1, -3, -1, -3, -1, 3, 0, 2, 0, 2, 0, 2, 0, 1, 0, 0, 0, 0, 0, -1, 0, 0, -1, 0, -1, 1, -2, 1, -2, -6, 0, -6, 0, -5, 1, -5, 1, -5, -2, -5, -3, -4, -2, -4, -2] from scitbx.array_family import flex total_tile_translations = flex.int(corrected_auxiliary_translations) TT = list(total_tile_translations) working_extract.distl.tile_translations = TT # Order: UL x, UL y, UR x, UR y, LL x, LL y, LR x, LR y working_extract.distl.quad_translations = [-6,-2,9,2,-14,-8,7,-12] return working_extract elif cxi_version in ["XPP 7.1"]: working_extract = working_phil.command_extractor corrected_auxiliary_translations = [ 0, 0, 0, 0, 0, 0, 0, 0, 0, -2, 0, -2, -1, -1, -1, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -2, -2, -2, -2, -1, -1, -1, -1, -1, -1, -1, -1, 0, 0, 0, 0, -2, -1, -2, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, 0, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, -1, -1, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] L748_corrections_post103 = [ 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, 0, -1, -1, 0, -1, 0, 1, -1, 1, -1, 0, 0, 0, 0, 0, 0, 0, 0, 2, 1, 2, 1, 0, 0, 0, 0, -1, 0, -1, 0, 3, 0, 3, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, -1, 1, -1, 0, 0, 0, 0, 0, 1, 0, 1, 1, 3, 1, 3, 1, 3, 1, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -2, 0, -2, 0, 0, 0, 0, ] # for 110 mm from scitbx.array_family import flex total_tile_translations = flex.int(corrected_auxiliary_translations) - \ flex.int(L748_corrections_post103) TT = list(total_tile_translations) working_extract.distl.tile_translations = TT # Order: UL x, UL y, UR x, UR y, LL x, LL y, LR x, LR y. For the # XPP CSPAD, this is effectively correcting for the beam center. working_extract.distl.quad_translations = [-3, -21, -3, -22, -3, -21, 2, -21] return working_extract elif cxi_version in ["XPP 8.1"]: working_extract = working_phil.command_extractor corrected_auxiliary_translations = [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] from scitbx.array_family import flex total_tile_translations = flex.int(corrected_auxiliary_translations) TT = list(total_tile_translations) working_extract.distl.tile_translations = TT # Order: UL x, UL y, UR x, UR y, LL x, LL y, LR x, LR y. For the # XPP CSPAD, this is effectively correcting for the beam center. working_extract.distl.quad_translations = [0, 1, 0, 1, 0, 1, 0, 1] return working_extract elif cxi_version in ["XPP 9.1"]: working_extract = working_phil.command_extractor # metrology from trial 14, runs 40, 41, xppe0314 corrected_auxiliary_translations = [ 1, 2, 1, 2, 1, 2, 1, 2, 2, 1, 2, 1, 2, 2, 2, 2, -1, -1, -1, -1, 0, 0, 0, 0, -2, 1, -2, 1, -1, 2, -1, 2, 0, -1, 0, -1, 0, 0, 0, 0, -2, -1, -2, -1, -2, -1, -2, -1, -2, 0, -2, 0, -3, -1, -3, -1, 0, -2, 0, -2, 0, -1, 0, -1, 1, -1, 1, -1, 1, -1, 1, -1, 0, -3, 0, -3, 1, -2, 1, -2, -2, -3, -2, -3, 0, 0, 0, 0, -3, 0, -3, 0, 0, -1, 0, -1, -1, 0, -1, 0, 0, 0, 0, 0, -3, 1, -3, 1, -3, 1, -3, 1, -1, 2, -1, 2, -4, 2, -4, 2, 0, 0, 0, 0, 0, -1, 0, -1 ] from scitbx.array_family import flex total_tile_translations = flex.int(corrected_auxiliary_translations) TT = list(total_tile_translations) working_extract.distl.tile_translations = TT # Order: UL x, UL y, UR x, UR y, LL x, LL y, LR x, LR y. For the # XPP CSPAD, this is effectively correcting for the beam center. # analysis by hand from run 40+41, xppe0314. #working_extract.distl.quad_translations = [3, -1, # 6, -1, # 4, -1, # 4, -5] # account for a change in beam center. offset 7 pixels in the x direction. # valid for runs 124, 126 working_extract.distl.quad_translations = [3, 6, 6, 6, 4, 6, 4, 1] return working_extract elif cxi_version in ["XPP 11.1"]: working_extract = working_phil.command_extractor # metrology from trial 14, runs 40, 41, xppe0314 corrected_auxiliary_translations = [ 1, 2, 1, 2, 1, 2, 1, 2, 2, 1, 2, 1, 2, 2, 2, 2, -1, -1, -1, -1, 0, 0, 0, 0, -2, 1, -2, 1, -1, 2, -1, 2, 0, -1, 0, -1, 0, 0, 0, 0, -2, -1, -2, -1, -2, -1, -2, -1, -2, 0, -2, 0, -3, -1, -3, -1, 0, -2, 0, -2, 0, -1, 0, -1, 1, -1, 1, -1, 1, -1, 1, -1, 0, -3, 0, -3, 1, -2, 1, -2, -2, -3, -2, -3, 0, 0, 0, 0, -3, 0, -3, 0, 0, -1, 0, -1, -1, 0, -1, 0, 0, 0, 0, 0, -3, 1, -3, 1, -3, 1, -3, 1, -1, 2, -1, 2, -4, 2, -4, 2, 0, 0, 0, 0, 0, -1, 0, -1 ] from scitbx.array_family import flex total_tile_translations = flex.int(corrected_auxiliary_translations) TT = list(total_tile_translations) working_extract.distl.tile_translations = TT # Order: UL x, UL y, UR x, UR y, LL x, LL y, LR x, LR y. For the # XPP CSPAD, this is effectively correcting for the beam center. # analysis by hand from runs 35-38, trial 1, xpph9015. working_extract.distl.quad_translations = [1, 10, 2, 9, -1, 9, -1, 4] return working_extract elif cxi_version in ["XPP 7.marccd"]: working_extract = working_phil.command_extractor working_extract.distl.quad_translations = None working_extract.distl.tile_translations = [0, 0] return working_extract elif cxi_version in ["CXI 8.1inheritedfrom7.1"]: working_extract = working_phil.command_extractor corrected_auxiliary_translations = [ 2, 1, 1, 1, 1, 2, 0, 2, 3, 0, 0, 0, 4, 1, 3, 1, 1, -2, 2, -1, -1, -1, 1, -1, -1, -2, -1, -1, -1, 0, -1, 1, -2, 0, 0, 1, 0, 0, 1, 1, -1, 1, -2, 1, -1, 0, -1, 1, -1, 1, -1, 1, -2, 1, -1, 1, 1, 1, 0, 2, -1, 1, 0, 1, 0, 1, 0, 1, 0, 0, 0, 1, -1, 0, 0, 1, 0, -1, -1, 1, -1, 0, -1, 1, -1, 0, -2, 0, 0, 1, 0, 1, -1, 0, 1, 0, 2, -1, 2, -1, 1, 0, 0, 0, 1, -1, 1, -2, 2, -2, 2, -2, 0, -1, 1, -1, 2, 1, 0, 0, 0, 0, 0, -2, 1, 1, 1, 0] from scitbx.array_family import flex total_tile_translations = flex.int(corrected_auxiliary_translations) TT = list(total_tile_translations) working_extract.distl.tile_translations = TT # Order: UL x, UL y, UR x, UR y, LL x, LL y, LR x, LR y working_extract.distl.quad_translations = [-22,-4,-14,11,0,8,2,-5] return working_extract elif cxi_version in ["CXI 8.1"]: # developed against "run 4 optical metrology" working_extract = working_phil.command_extractor corrected_auxiliary_translations = [ -2, -3, -2, -3, -3, -3, -3, -3, -4, -4, -4, -4, -2, -4, -2, -4, -2, -2, -2, -2, 0, 0, -1, 1, -4, -2, -4, -2, -3, 0, -3, 0, -4, 2, -4, 2, -4, 2, -4, 2, -5, 3, -5, 3, -5, 3, -5, 3, -2, 3, -2, 3, 3, 1, 3, 1, -1, 2, -1, 2, -2, 1, -2, 1, 3, 3, 3, 3, 2, 3, 2, 3, 2, 3, 2, 3, 2, 2, 2, 2, 2, 4, 2, 4, 0, -1, -1, 0, 3, 3, 3, 3, 2, 2, 2, 2, 4, -3, 4, -3, 4, -3, 4, -3, 3, -3, 4, -3, 3, -3, 4, -3, -2, -1, -2, -2, -3, 2, -3, 2, 1, -3, 1, -3, 2, -2, 2, -2, ] from scitbx.array_family import flex total_tile_translations = flex.int(corrected_auxiliary_translations) TT = list(total_tile_translations) working_extract.distl.tile_translations = TT # Order: UL x, UL y, UR x, UR y, LL x, LL y, LR x, LR y # Note, these numbers are valid for the CSPAD detector at roughly 100 mm distance working_extract.distl.quad_translations = [-14,7,-4,7,-22,0,-12,-4] # Calibrated at 201 #working_extract.distl.quad_translations = [-14,7,-4,6,-23,0,-13,-5] # Due to a slight angle in the rail, if the detector is at the back of its # stage, around 548 mm, use these numbers instead. They represent a change # of beam center due to a small translation at that distance #working_extract.distl.quad_translations = [-10,5,0,5,-18,-2,-8,-6] # Recalibration of 548 mm vs run 111 of lysozyme calibration dataset #working_extract.distl.quad_translations = [-11,4,-2,6,-18,-3,-9,-4] return working_extract elif cxi_version in ["CXI 8.2"]: working_extract = working_phil.command_extractor corrected_auxiliary_translations = [ 1, 7, 1, 7, -1, 0, -1, 0, 5, 4, 5, 4, 1, 4, 1, 4, 6, -2, 6, -2, 5, 3, 5, 3, 5, 0, 5, 0, 0, 3, 0, 3, 4, 0, 4, 0, 1, 0, 1, 0, 3, -7, 3, -7, 3, -1, 3, -1, -1, -5, -1, -5, 6, -4, 6, -4, 2, -3, 2, -3, 2, -4, 2, -4, -1, -5, -1, -5, 0, 0, 0, 0, -10, 0,-10, 0, -1, -1, -1, -1, -5, 8, -5, 8, -8, 2, -8, 2, -1, 2, -1, 2, -2, 1, -2, 1, -7, 0, -7, 0, -1, 0, -1, 0, -6, 4, -6, 4, -4, -6, -4, -6, -3, 2, -3, 2, -8, 3, -8, 3, -4, 6, -4, 6, -4, 2, -4, 2] LC06_mark10_001_corrections = [ 0, 0, 0, 0, 0, -1, 0, -1, -1, 1, -1, 1, -1, 1, -1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 1, 2, 1, 0, 1, 0, -1, 0, -1, 0, -1, 0, -1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 2, 1, 2, 0, 1, 0, 1, 0, 1, 0, 1, 0, 2, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, -1, 1, -1, 1, -1, 1, -1, 0, -2, 0, -2, 1, -2, 1, -2, 0, 0, 0, 0, 0, 0, 0, 0, -1, 2, -1, 2, -1, 0, -1, 0] # for 79 mm LC06_mark10_101_corrections = [ 0, 0, 0, 0, 0, -1, 0, -1, -1, 0, -1, 0, -0, 0, -0, 0, 0, 1, 0, 1, 2, 2, 2, 2, 0, 1, 0, 1, 0, 0, 0, 0, -1, 0, -1, 0, -1, 0, -1, 0, -1, 0, -1, 0, -1, 1, -1, 1, -1, 0, -1, 0, 0, 1, 0, 1, -1, 0, -1, 0, 0, 0, 0, 0, 0, 2, 0, 2, 0, 1, 0, 1, 0, 1, 0, 1, 0, 3, 0, 3, 1, 2, 1, 2, 1, 3, 1, 3, 0, 1, 0, 1, 0, 1, 0, 1, 1, -1, 1, -1, 1, -1, 1, -1, 0, -2, 0, -2, 2, -2, 2, -2, 0, -1, 0, -1, 0, -2, 0, -2, -0, 0, -0, 0, -0, 0, -0, 0] # for 159 mm LB67_corrections_post009 = [ 1, 0, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 2, 3, 2, 4, 2, 4, 2, 2, 2, 2, 1, 0, 1, 0, -1, 0, -1, 0, 0, 0, 0, 0, 0, -1, 0, -1, 0, 0, 0, 0, 0, -1, 0, -1, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, -1, 0, -1, 0, -1, 1, -1, 1, -1, 2, -1, 2, 0, 1, 0, 1, 0, 2, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 1, -1, 1, -1, 0, -1, 0, -1, 0, -1, 0, -1, 1, -1, 1, -1, -2, 0, -2, 0, -2, -1, -2, -1, -1, 1, -1, 1, -1, -1, -1, -1,] # for 105 mm from scitbx.array_family import flex total_tile_translations = flex.int(corrected_auxiliary_translations) - \ flex.int(LB67_corrections_post009) # flex.int(LC06_mark10_001_corrections) # flex.int(LC06_mark10_101_corrections) TT = list(total_tile_translations) working_extract.distl.tile_translations = TT # Order: UL x, UL y, UR x, UR y, LL x, LL y, LR x, LR y. Optimized for 267 mm. #working_extract.distl.quad_translations = [-3, 2, # -8, 3, # -7, 8, # -10, 8] # determined for LC06_runs15-17. Optimized for 159 mm #working_extract.distl.quad_translations = [-2, 1, # -9, 3, # -5, 8, # -9, 10] # determined for LC67_run26. Optimized for 101 mm; detz_offset must be changed to move 100 mm distance to 101 working_extract.distl.quad_translations = [ 0, 3, -7, 3, -5, 9, -9, 9] # Order: UL x, UL y, UR x, UR y, LL x, LL y, LR x, LR y. Optimized for 79 mm. #working_extract.distl.quad_translations = [-2, 3, # -9, 5, # -5, 10, # -9, 12] return working_extract elif cxi_version in ["CXI 9.1"]: working_extract = working_phil.command_extractor from scitbx.array_family import flex # Based on the LD91 experiment, runs 95-114, redetermined 3/17/15 NKS corrected_auxiliary_translations = flex.int([ 0, 8, 0, 8, -1, -1, -1, -1, 8, 2, 8, 2, 3, 2, 3, 2, 5, -6, 5, -6, 3, -1, 3, -1, 2, -1, 2, -1, -2, 1, -2, 1, 4, 1, 4, 1, 1, 1, 1, 1, 0, -7, 0, -7, 2, -2, 2, -2, -1, -4, -1, -4, 8, -4, 8, -4, 7, -7, 7, -7, 7, -1, 7, -1, 1, -5, 1, -5, 2, -1, 2, -1, -8, -3, -8, -3, -1, -5, -1, -5, -4, 6, -4, 6, -7, -3, -7, -3, -7, 1, -7, 1, 1, -1, 1, -1, -8, 3, -8, 3, 0, 1, 0, 1, -3, 8, -3, 8, -4, 1, -4, 1, 0, 6, 0, 6, -7, 7, -7, 7, -3, 2, -3, 2, -3, 3, -3, 3]) working_extract.distl.tile_translations = list(corrected_auxiliary_translations) # Order: UL x, UL y, UR x, UR y, LL x, LL y, LR x, LR y. # Determined for LD91 run 33. Optimized for 125 mm working_extract.distl.quad_translations = [ 8, -3, -9, 5, 9, 7, -5, 15] return working_extract elif cxi_version in ["CXI 8.d"]: working_extract = working_phil.command_extractor from scitbx.array_family import flex total_tile_translations = flex.int(128) TT = list(total_tile_translations) working_extract.distl.tile_translations = TT # Order: UL x, UL y, UR x, UR y, LL x, LL y, LR x, LR y. working_extract.distl.quad_translations = [11, 3, -3, -2, 0, 8, 0, 4] print(len(working_extract.distl.tile_translations)) return working_extract elif cxi_version in ["CXI 10.1"]: working_extract = working_phil.command_extractor from scitbx.array_family import flex # Determined from LG36, trial 305 corrected_auxiliary_translations =flex.int([ 1, 6, 1, 6, 0, 0, 0, 0, 6, 1, 6, 1, 2, 2, 2, 2, 5, -6, 5, -6, 3, -3, 3, -3, 3, -3, 3, -3, -1, 2, -1, 2, 4, 0, 4, 0, 0, 0, 0, 0, 2, -7, 2, -7, 2, -1, 2, -1, -3, -7, -3, -7, 3, -6, 3, -6, 1, -9, 1, -9, 0, -2, 0, -2, 0, -6, 0, -6, 0, 0, 0, 0, -10, -1,-10, -1, -1, -3, -1, -3, -7, 5, -7, 5, 0, 0, 0, 0, -7, -2, -7, -2, -1, -2, -1, -2, -7, 0, -7, 0, 0, 0, 0, 0, -5, 6, -5, 6, -5, -4, -5, -4, -1, 3, -1, 3, 1, -1, 1, -1, -3, 5, -3, 5, -2, 1, -2, 1]) working_extract.distl.tile_translations = list(corrected_auxiliary_translations) # Order: UL x, UL y, UR x, UR y, LL x, LL y, LR x, LR y. # Determined for LG36 run 82. Optimized for 118 mm working_extract.distl.quad_translations = [8, 3, 5, 3, 7, 11, 3, 12] return working_extract elif cxi_version in ["CXI 10.2"]: working_extract = working_phil.command_extractor from scitbx.array_family import flex corrected_auxiliary_translations =flex.int([ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]) working_extract.distl.tile_translations = list(corrected_auxiliary_translations) # Order: UL x, UL y, UR x, UR y, LL x, LL y, LR x, LR y. # Determined for LG36 run 82. Optimized for 118 mm working_extract.distl.quad_translations = [ 0, 0, 0, 0, 0, 0, 0, 0] return working_extract elif cxi_version in ["CXI 11.1"]: working_extract = working_phil.command_extractor from scitbx.array_family import flex corrected_auxiliary_translations =flex.int([ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]) working_extract.distl.tile_translations = list(corrected_auxiliary_translations) # Order: UL x, UL y, UR x, UR y, LL x, LL y, LR x, LR y. working_extract.distl.quad_translations = [ 0, 0, 0, 0, 0, 0, 0, 0] return working_extract elif cxi_version in ["CXI 11.2"]: working_extract = working_phil.command_extractor from scitbx.array_family import flex # Determined from LH80, runs 18-23, trial 014_000 """ corrected_auxiliary_translations =flex.int([ 2, 1, 2, 1, 1, 2, 1, 2, 3, 0, 3, 0, 2, 0, 2, 0, 1, 0, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 1, 0, 1, -1, 0, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, -1, -1, -1, 2, -2, 2, -2, 0, 0, 0, 0, 1, -3, 1, -3, 0, 0, 0, 0, 0, -3, 0, -3, 0, -2, 0, -2, -2, -4, -2, -4, -1, -3, -1, -3, -2, -3, -2, -3, 0, 0, 0, 0, -3, -1, -3, -1, -1, -2, -1, -2, -1, 2, -1, 2, -2, 1, -2, 1, -2, 2, -2, 2, -3, 2, -3, 2, -2, 2, -2, 2, 0, 0, 0, 0, -1, -2, -1, -2, -1, 0, -1, 0]) """ # Determined from LH80, runs 46-51, trial 019_000 corrected_auxiliary_translations =flex.int([ 2, 1, 2, 1, 2, 2, 2, 2, 2, -2, 2, -2, 2, -1, 2, -1, -1, -2, -1, -2, -3, -6, -3, -6, -1, 1, -1, 1, 0, 1, 0, 1, -2, 1, -2, 1, -1, 0, -1, 0, # row from 014_001 # 0, 0, 0, 0, -1, -1, -1, -1, # original row from 019_000 #-2, 1, -2, 1, -3, 0, -3, 0, # the minus 2s and 3s above put this sensor off of the edge. 0, 1, 0, 1, -1, 0, -1, 0, 1, -2, 1, -2, 1, -1, 1, -1, 1, -4, 1, -4, 0, 0, 0, 0, 1, -3, 1, -3, 0, -2, 0, -2, -1, -5, -1, -5, 0, -4, 0, -4, -3, -4, -3, -4, -3, -6, -3, -6, -1, -1, -1, -1, 0, -2, 0, -2, -1, 1, -1, 1, -2, 1, -2, 1, -2, 1, -2, 1, -3, 1, -3, 1, -1, 0, -1, 0, 0, 0, 0, 0, 0, -3, 0, -3, -1, 0, -1, 0]) working_extract.distl.tile_translations = list(corrected_auxiliary_translations) # Order: UL x, UL y, UR x, UR y, LL x, LL y, LR x, LR y. # Manually determined from LH80 run 12. Optimized for 85 mm #working_extract.distl.quad_translations = [-11, 2, # -8, 2, # -9, 2, # -11, 4] # Manually determined from LH80 runs 31-37. Optimized for 85 mm. Good for runs 31+ working_extract.distl.quad_translations = [-16, 5, -11, 5, -14, 5, -16, 6] return working_extract elif cxi_version in ["Sacla.MPCCD"]: working_extract = working_phil.command_extractor working_extract.distl.quad_translations = None working_extract.distl.tile_translations = None return working_extract elif cxi_version in ["Sacla.MPCCD.8tile"]: working_extract = working_phil.command_extractor working_extract.distl.quad_translations = None from scitbx.array_family import flex corrected_auxiliary_translations =flex.int([ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ]) working_extract.distl.tile_translations = list(corrected_auxiliary_translations) #working_extract.distl.tile_translations = None return working_extract else: return working_phil.command_extractor