from __future__ import division, unicode_literals, print_function,\ absolute_import ''' Author : Lyubimov, A.Y. Created : 05/25/2016 Last Changed: 07/17/2019 Description : PRIME Result Plotter module ''' import numpy as np from matplotlib import gridspec, rc from iota.gui.plotter import Plotter as IOTAPlotter class Plotter(IOTAPlotter): ''' Class with function to plot various PRIME charts (includes Table 1) ''' def __init__(self, parent, info, output_dir=None, anomalous_flag=False, *args, **kwargs): super(Plotter, self).__init__(parent=parent, info=info, *args, **kwargs) self.target_anomalous_flag = anomalous_flag self.output_dir = output_dir def table_one(self, as_tex=False): ''' Constructs Table 1 for GUI or logging ''' if as_tex: A = r'$\AA$' d = r'$\circ$' a = r'$\alpha$' b = r'$\beta$' g = r'$\gamma$' s = r'$\sigma$' h = r'$\frac{1}{2}$' rm = r'$\_merge$' else: A = '\N{ANGSTROM SIGN}' d = '\N{DEGREE SIGN}' a = '\N{GREEK SMALL LETTER ALPHA}' b = '\N{GREEK SMALL LETTER BETA}' g = '\N{GREEK SMALL LETTER GAMMA}' s = '\N{GREEK SMALL LETTER SIGMA}' h = '\u00BD' rm = '_merge' t1_rlabels = ['No. of accepted images', 'No. of rejected images', 'Space Group', 'Cell dimensions', ' a, b, c ({}) '.format(A), ' {}, {}, {} ({}) '.format(a, b, g, d), 'Resolution ({}) '.format(A), 'Completeness (%)', 'Multiplicity', 'I / {}(I) '.format(s), 'CC{} '.format(h), 'R{}'.format(rm)] uc_edges = '{:4.2f}, {:4.2f}, {:4.2f}'.format(self.info['mean_a'][-1], self.info['mean_b'][-1], self.info['mean_c'][-1]) uc_angles = '{:4.2f}, {:4.2f}, {:4.2f}'.format(self.info['mean_alpha'][-1], self.info['mean_beta'][-1], self.info['mean_gamma'][-1]) res_total = '{:4.2f} - {:4.2f}'.format(self.info['total_res_max'][-1], self.info['total_res_min'][-1]) res_last_shell = '{:4.2f} - {:4.2f}' \ ''.format(self.info['binned_resolution'][-1][-2], self.info['binned_resolution'][-1][-1]) n_frames_bad = self.info['n_frames_bad_cc'][-1] + \ self.info['n_frames_bad_G'][-1] + \ self.info['n_frames_bad_uc'][-1] + \ self.info['n_frames_bad_gamma_e'][-1] + \ self.info['n_frames_bad_SE'][-1] t1_data = [['{}'.format(self.info['n_frames_good'][-1])], ['{}'.format(n_frames_bad)], ['{}'.format(self.info['space_group_info'][-1])], [''], ['{}'.format(uc_edges)], ['{}'.format(uc_angles)], ['{} ({})'.format(res_total, res_last_shell)], ['{:4.2f} ({:4.2f})'.format(self.info['total_completeness'][-1], self.info['binned_completeness'][-1][-1])], ['{:4.2f} ({:4.2f})'.format(self.info['total_n_obs'][-1], self.info['binned_n_obs'][-1][-1])], ['{:4.2f} ({:4.2f})'.format(self.info['total_i_o_sigi'][-1], self.info['binned_i_o_sigi'][-1][-1])], ['{:4.2f} ({:4.2f})'.format(self.info['total_cc12'][-1], self.info['binned_cc12'][-1][-1]*100)], ['{:4.2f} ({:4.2f})'.format(self.info['total_rmerge'][-1], self.info['binned_rmerge'][-1][-1])] ] return t1_rlabels, t1_data def flatten_table_one_data(self, as_tex=False): rlabels, tb1_data = self.table_one(as_tex=as_tex) # Flatten data list of lists (works this once, since each sub-list # contains a single item) tb1_data = list(zip(*tb1_data))[0] data = list(zip(rlabels, tb1_data)) return data def table_one_text(self): data = self.flatten_table_one_data() return self.plot_table_text(data=data) def table_one_figure(self): data = self.flatten_table_one_data() self.plot_table(data=data) def stat_charts(self): ''' Displays charts of CC1/2, Completeness, Multiplicity and I / sig(I) per resolution bin after the final cycle of post-refinement ''' gsp = gridspec.GridSpec(2, 2) gsp.update(wspace=0.1, hspace=0.1) self.figure.set_alpha(0) rc('font', family='sans-serif', size=12) rc('mathtext', default='regular') x = self.info['binned_resolution'][-1] bins = np.arange(len(x)) xlabels = ["{:.2f}".format(i) for i in x] sel_bins = bins[0::len(bins) // 6] sel_xlabels = [xlabels[t] for t in sel_bins] # Plot CC1/2 vs. resolution ax_cc12 = self.figure.add_subplot(gsp[0]) reslabel = 'Resolution ({})'.format(r'$\AA$') ax_cc12.set_xlabel(reslabel, fontsize=15) ax_cc12.ticklabel_format(axis='y', style='plain') ax_cc12.set_ylim(0, 100) if self.target_anomalous_flag: ax_cc12.set_ylabel(r'$CC_{1/2}$ anom (%)', fontsize=15) else: ax_cc12.set_ylabel(r'$CC_{1/2}$ (%)', fontsize=15) ax_cc12.set_xticks(sel_bins) ax_cc12.set_xticklabels(sel_xlabels) ax_cc12.grid(True) cc12_start_percent = [c * 100 for c in self.info['binned_cc12'][0]] cc12_end_percent = [c * 100 for c in self.info['binned_cc12'][-1]] start, = ax_cc12.plot(bins, cc12_start_percent, c='#7fcdbb', lw=2) end, = ax_cc12.plot(bins, cc12_end_percent, c='#2c7fb8', lw=3) labels = ['Initial', 'Final'] ax_cc12.legend([start, end], labels, loc='lower left', fontsize=9, fancybox=True) # Plot Completeness vs. resolution ax_comp = self.figure.add_subplot(gsp[1]) ax_comp.set_xlabel(reslabel, fontsize=15) ax_comp.ticklabel_format(axis='y', style='plain') ax_comp.set_ylabel('Completeness (%)', fontsize=15) ax_comp.set_xticks(sel_bins) ax_comp.set_xticklabels(sel_xlabels) ax_comp.set_ylim(0, 100) ax_comp.grid(True) start, = ax_comp.plot(bins, self.info['binned_completeness'][0], c='#7fcdbb', lw=2) end, = ax_comp.plot(bins, self.info['binned_completeness'][-1], c='#2c7fb8', lw=3) labels = ['Initial', 'Final'] ax_comp.legend([start, end], labels, loc='lower left', fontsize=9, fancybox=True) # Plot Multiplicity (no. of observations) vs. resolution ax_mult = self.figure.add_subplot(gsp[2]) ax_mult.set_xlabel(reslabel, fontsize=15) ax_mult.ticklabel_format(axis='y', style='plain') ax_mult.set_ylabel('# of Observations', fontsize=15) ax_mult.set_xticks(sel_bins) ax_mult.set_xticklabels(sel_xlabels) ax_mult.grid(True) start, = ax_mult.plot(bins, self.info['binned_n_obs'][0], c='#7fcdbb', lw=2) end, = ax_mult.plot(bins, self.info['binned_n_obs'][-1], c='#2c7fb8', lw=3) labels = ['Initial', 'Final'] ax_mult.legend([start, end], labels, loc='lower left', fontsize=9, fancybox=True) # Plot I / sig(I) vs. resolution ax_i_sigi = self.figure.add_subplot(gsp[3]) ax_i_sigi.set_xlabel(reslabel, fontsize=15) ax_i_sigi.ticklabel_format(axis='y', style='plain') ax_i_sigi.set_ylabel(r'I / $\sigma$(I)', fontsize=15) ax_i_sigi.set_xticks(sel_bins) ax_i_sigi.set_xticklabels(sel_xlabels) ax_i_sigi.grid(True) start, = ax_i_sigi.plot(bins, self.info['binned_i_o_sigi'][0], c='#7fcdbb', lw=2) end, = ax_i_sigi.plot(bins, self.info['binned_i_o_sigi'][-1], c='#2c7fb8', lw=3) labels = ['Initial', 'Final'] ax_i_sigi.legend([start, end], labels, loc='lower left', fontsize=9, fancybox=True) # self.figure.set_tight_layout(True) self.draw(tight_layout=False)