farrow

15 - def __init__(self, mf):

16 "The model-free analysis of Farrow." 17 18 self.mf = mf 19 20 print "Farrow's method for model-free analysis. (Farrow et al., 1994)" 21 self.initialize() 22 self.mf.data.runs = ['m1', 'm2', 'm3', 'm4', 'm5', 'f-m1m2', 'f-m1m3'] 23 if self.mf.data.num_data_sets > 3: 24 self.mf.data.runs.append('f-m2m4') 25 self.mf.data.runs.append('f-m2m5') 26 self.mf.data.runs.append('f-m3m4') 27 self.goto_stage()

28 29

30 - def initial_runs(self):

31 "Creation of the files for the Modelfree calculations for models 1 to 5 and the F-tests." 32 33 for run in self.mf.data.runs: 34 if match('^m', run): 35 print "Creating input files for model " + run 36 self.mf.log.write("\n\n<<< Model " + run + " >>>\n\n") 37 elif match('^f', run): 38 print "Creating input files for the F-test " + run 39 self.mf.log.write("\n\n<<< F-test " + run + " >>>\n\n") 40 else: 41 print "The run '" + run + "'does not start with an m or f, quitting script!\n\n" 42 sys.exit() 43 self.mf.file_ops.mkdir(dir=run) 44 self.mf.file_ops.open_mf_files(dir=run) 45 self.set_run_flags(run) 46 self.log_params('M1', self.mf.data.usr_param.md1) 47 self.log_params('M2', self.mf.data.usr_param.md2) 48 if match('^m', run): 49 self.create_mfin(sims='y', sim_type='pred') 50 elif match('^f', run): 51 self.create_mfin(sel='ftest', sims='y', sim_type='pred') 52 self.create_run(dir=run) 53 for res in range(len(self.mf.data.relax_data[0])): 54 # Mfdata. 55 self.create_mfdata(res) 56 # Mfmodel. 57 self.create_mfmodel(res, self.mf.data.usr_param.md1, type='M1') 58 if match('^f', run): 59 self.create_mfmodel(res, self.mf.data.usr_param.md2, type='M2') 60 # Mfpar. 61 self.create_mfpar(res) 62 self.mf.file_ops.close_mf_files(dir=run)

63 64

65 - def model_selection(self):

66 "Farrow's model selection." 67 68 data = self.mf.data.data 69 70 self.mf.log.write("\n\n<<< Farrow's model selection >>>") 71 for res in range(len(self.mf.data.relax_data[0])): 72 self.mf.data.results.append({}) 73 self.mf.log.write('\n%-22s' % ( " Checking res " + data['m1'][res]['res_num'] )) 74 75 # Model 1 test. 76 if data['m1'][res]['sse_test'] == 1: 77 self.mf.log.write('%-12s' % '[Model 1]') 78 self.mf.data.results[res] = self.fill_results(data['m1'][res], model='1') 79 80 # Test if both model 2 and 3 fit!!! (Should not occur) 81 elif data['m2'][res]['sse_test'] == 1 and data['f-m1m2'][res]['ftest'] == 1 \ 82 and data['m3'][res]['sse_test'] == 1 and data['f-m1m3'][res]['ftest'] == 1: 83 self.mf.log.write('%-12s' % '[Model 2 and 3]') 84 self.mf.data.results[res] = self.fill_results(data['m1'][res], model='2+3') 85 86 # Model 2 test. 87 elif data['m2'][res]['sse_test'] == 1 and data['f-m1m2'][res]['ftest'] == 1: 88 self.mf.log.write('%-12s' % '[Model 2]') 89 self.mf.data.results[res] = self.fill_results(data['m2'][res], model='2') 90 91 # Model 3 test. 92 elif data['m3'][res]['sse_test'] == 1 and data['f-m1m3'][res]['ftest'] == 1: 93 self.mf.log.write('%-12s' % '[Model 3]') 94 self.mf.data.results[res] = self.fill_results(data['m3'][res], model='3') 95 96 # Large SSE test for model 1. 97 elif data['m1'][res]['large_sse'] == 0: 98 self.mf.log.write('%-12s' % '[Model 1*]') 99 self.mf.data.results[res] = self.fill_results(data['m1'][res], model='1') 100 101 # Test if both model 4 and 5 fit!!! (Should not occur) 102 elif data['m4'][res]['zero_sse'] == 1 and data['m5'][res]['zero_sse'] == 1: 103 self.mf.log.write('%-12s' % '[Model 4 and 5]') 104 self.mf.data.results[res] = self.fill_results(data['m1'][res], model='4+5') 105 106 # Model 4 test. 107 elif data['m4'][res]['zero_sse'] == 1: 108 self.mf.log.write('%-12s' % '[Model 4]') 109 self.mf.data.results[res] = self.fill_results(data['m4'][res], model='4') 110 111 # Model 5 test. 112 elif data['m5'][res]['zero_sse'] == 1: 113 self.mf.log.write('%-12s' % '[Model 5]') 114 self.mf.data.results[res] = self.fill_results(data['m5'][res], model='5') 115 116 # No model fits! 117 else: 118 self.mf.log.write('%-12s' % '[Model 0]') 119 self.mf.data.results[res] = self.fill_results(data['m1'][res], model='0')

120 121

122 - def stage2(self):

123 self.mf.file_ops.mkdir('grace') 124 125 print "\n[ Model-free data extraction ]\n" 126 for run in self.mf.data.runs: 127 mfout = self.mf.file_ops.read_file(run + '/mfout') 128 mfout_lines = mfout.readlines() 129 mfout.close() 130 print "Extracting model-free data from " + run + "/mfout." 131 num_res = len(self.mf.data.relax_data[0]) 132 if match('^m', run): 133 self.mf.data.data[run] = self.mf.star.extract(mfout_lines, num_res, self.mf.data.usr_param.sse_lim, self.mf.data.usr_param.ftest_lim, float(self.mf.data.usr_param.large_sse), ftest='n') 134 if match('^f', run): 135 self.mf.data.data[run] = self.mf.star.extract(mfout_lines, num_res, self.mf.data.usr_param.sse_lim, self.mf.data.usr_param.ftest_lim, float(self.mf.data.usr_param.large_sse), ftest='y') 136 137 print "\n[ Farrow's model selection ]\n" 138 self.mf.log.write("Farrow's model selection.\n\n") 139 self.model_selection() 140 141 print "\n[ Printing results ]\n" 142 self.print_results() 143 144 print "\n[ Placing data structures into \"data_all\" ]\n" 145 self.print_data(ftests='y') 146 147 print "\n[ Grace file creation ]\n" 148 self.grace('grace/S2.agr', 'S2', subtitle="After model selection, unoptimized") 149 self.grace('grace/S2f.agr', 'S2f', subtitle="After model selection, unoptimized") 150 self.grace('grace/S2s.agr', 'S2s', subtitle="After model selection, unoptimized") 151 self.grace('grace/te.agr', 'te', subtitle="After model selection, unoptimized") 152 self.grace('grace/Rex.agr', 'Rex', subtitle="After model selection, unoptimized") 153 self.grace('grace/SSE.agr', 'SSE', subtitle="After model selection, unoptimized")

Source Code for Module farrow