from __future__ import absolute_import, division, print_function from six.moves import range from scitbx.array_family import flex from scitbx import matrix from six.moves import zip """Standalone program gives tile translations for the CXI pad detector; based on lysozyme test powder arcs. Fixed coordinates for the detector center (850,850) are simply based on CXI output file size. distl.detector_tiling limits are based on a separate run of the program spotfinder.find_active_area coordinates of pixels on the powder arcs of all four quadrants were obtained by manual inspection. 200 XFEL shots with the highest count of spotfinder spots were summed and inspected with the phenix.image_viewer. """ init_ctr_slow = 850 init_ctr_fast = 850 init_ctr = matrix.col([init_ctr_slow,init_ctr_fast]) class quadrant: def __init__(self,arcs): self.arcs = arcs def refine_center_from_arcs(self): #initial guess for center, based on given size of Numpy arra init_ctr_slow = 850 init_ctr_fast = 850 init_ctr = matrix.col([init_ctr_slow,init_ctr_fast]) self.x = flex.double([init_ctr_slow,init_ctr_fast]) #add a radius parameter for each arc for arc in self.arcs: sample_point = matrix.col(arc.points[0]) guess_radius = (sample_point - init_ctr).length() self.x.append(guess_radius) self.initial_functional = None import scitbx.lbfgs scitbx.lbfgs.run(target_evaluator=self) self.final_functional = self.compute_functional_and_gradients( functional_only=True) def compute_functional_and_gradients(self, functional_only=False): def get_f(): center = matrix.col([self.x[0],self.x[1]]) residual = 0.0 for arc,radius in zip(self.arcs,self.x[2:]): for point in arc.points: ppoint = matrix.col(point) rad_vector = ppoint - center length = rad_vector.length() residual += (length-radius)*(length-radius) return residual f = get_f() if (self.initial_functional is None): self.initial_functional = f if (functional_only): return f g = flex.double() g.reserve(len(self.x)) eps = 1e-6 for i in range(len(self.x)): xi = self.x[i] self.x[i] = xi+eps f_eps = get_f() self.x[i] = xi g.append((f_eps-f)/eps) return f, g def show_summary(self): print("The center is %7.2f %7.2f; "%(self.x[0],self.x[1]), end=' ') print("radii are",[round(xx,2) for xx in self.x[2:]]) def get_tile_translation(self): slow_translation = int(float(init_ctr_slow) - self.x[0]) fast_translation = int(float(init_ctr_fast) - self.x[1]) return (slow_translation,fast_translation) def parse(string): words = string.split() values = [] for x in range(len(words)//2): values.append((int(words[2*x]),int(words[2*x+1]))) return values class powder_arc: def __init__(self,points): self.points = flex.vec2_double(parse(points)) print(list(self.points)) def lysozyme_calibration(): quad_1_UL= quadrant([ powder_arc(""" 844 729 815 731 788 740 759 764 738 796 """), powder_arc(""" 752 799 761 784 779 764 802 751 837 742 """), powder_arc(""" 839 754 816 758 792 769 775 783 763 800 """), powder_arc(""" 804 808 813 801 828 794 841 793 """), powder_arc(""" 816 809 823 805 833 801 845 802 """), ]) quad_1_UL_first_attempt = quadrant([ powder_arc(""" 846 728 814 731 790 740 760 761"""), powder_arc(""" 836 755 822 757 802 763 788 771"""), powder_arc(""" 787 794 799 784 810 776 825 772"""), powder_arc(""" 846 793 832 794 822 797 812 802"""), ]) quad_2_UR = quadrant([ powder_arc(""" 798 856 800 875 805 886 815 898 """), powder_arc(""" 775 864 778 884 787 902 799 915 """), powder_arc(""" 759 863 763 889 773 908 783 922 """), powder_arc(""" 734 873 740 900 748 918 809 968 """), powder_arc(""" 697 884 718 943 768 992 802 1005 """), ]) quad_3_LR = quadrant([ powder_arc(""" 854 925 867 925 886 919 896 914"""), powder_arc(""" 867 937 880 933 896 927 909 919 """), powder_arc(""" 923 941 904 954 885 959 860 963 """), powder_arc(""" 973 943 959 959 939 977 883 998 """), ]) quad_4_LL = quadrant([ powder_arc(""" 914 700 948 719 998 790 1007 831 """), powder_arc(""" 929 753 952 780 964 807 968 831 """), powder_arc(""" 942 841 941 815 931 795 897 762 """), powder_arc(""" 897 776 913 789 928 815 931 838 """), ]) quadrants = [quad_1_UL,quad_2_UR,quad_3_LR,quad_4_LL] for quad in quadrants: quad.refine_center_from_arcs() quad.show_summary() return derive_tile_translations(quadrants) def derive_tile_translations(quads): params = get_initial_cxi_scope() tile_list=[] tile_translations=[] tile_flags=[] for itile in range(len(params.distl.detector_tiling)//4): corner_UL = matrix.col([params.distl.detector_tiling[itile*4], params.distl.detector_tiling[itile*4+1]]) corner_LR = matrix.col([params.distl.detector_tiling[itile*4+2], params.distl.detector_tiling[itile*4+3]]) middle = (corner_UL + corner_LR)/2. if middle[0]init_ctr_fast: tile_list.append(2) #quadrant 2, UR elif middle[0]>init_ctr_slow and middle[1]>init_ctr_fast: tile_list.append(3) #quadrant 3, LR else: tile_list.append(4) #quadrant 4, LL translation = quads[tile_list[-1]-1].get_tile_translation() tile_translations.append(translation[0]) tile_translations.append(translation[1]) #finished with tile translations; now output flags for the actual tiles # where powder arcs have been observed (the inner four tiles) this_quad = quads[tile_list[-1]-1] first_point = this_quad.arcs[0].points[0] if corner_UL[0]