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24 """The automatic relaxation curve fitting protocol."""
25
26
27 from os import sep
28
29
30 from generic_fns.pipes import cdp_name, has_pipe, switch
31 import generic_fns.structure.main
32 from prompt.interpreter import Interpreter
33 from status import Status; status = Status()
34
35
36
38 - def __init__(self, pipe_name=None, pipe_bundle=None, file_root='rx', results_dir=None, grid_inc='11', mc_sim_num=500, view_plots=True):
39 """Perform relaxation curve fitting.
40
41 To use this auto-analysis, a data pipe with all the required data needs to be set up. This data pipe should contain the following:
42
43 - All the spins loaded.
44 - Unresolved spins deselected.
45 - All the peak intensities loaded and relaxation delay times set.
46 - Either the baseplane noise RMDS values should be set or replicated spectra loaded.
47
48 @keyword pipe_name: The name of the data pipe containing all of the data for the analysis.
49 @type pipe_name: str
50 @keyword pipe_bundle: The data pipe bundle to associate all spawned data pipes with.
51 @type pipe_bundle: str
52 @keyword file_root: File root of the output filea.
53 @type file_root: str
54 @keyword results_dir: The directory where results files are saved.
55 @type results_dir: str
56 @keyword grid_inc: Number of grid search increments.
57 @type grid_inc: int
58 @keyword mc_sim_num: The number of Monte Carlo simulations to be used for error analysis at the end of the analysis.
59 @type mc_sim_num: int
60 @keyword view_plots: Flag to automatically view grace plots after calculation.
61 @type view_plots: bool
62 """
63
64
65 status.exec_lock.acquire(pipe_bundle, mode='auto-analysis')
66
67
68 status.init_auto_analysis(pipe_bundle, type='relax_fit')
69 status.current_analysis = pipe_bundle
70
71
72 self.pipe_name = pipe_name
73 self.pipe_bundle = pipe_bundle
74 self.file_root = file_root
75 self.results_dir = results_dir
76 if self.results_dir:
77 self.grace_dir = results_dir + sep + 'grace'
78 else:
79 self.grace_dir = 'grace'
80 self.mc_sim_num = mc_sim_num
81 self.grid_inc = grid_inc
82 self.view_plots = view_plots
83
84
85 self.check_vars()
86
87
88 if self.pipe_name != cdp_name():
89 switch(self.pipe_name)
90
91
92 self.interpreter = Interpreter(show_script=False, quit=False, raise_relax_error=True)
93 self.interpreter.populate_self()
94 self.interpreter.on(verbose=False)
95
96
97 self.run()
98
99
100 status.auto_analysis[self.pipe_bundle].fin = True
101 status.current_analysis = None
102 status.exec_lock.release()
103
104
106 """Set up and run the curve-fitting."""
107
108
109 self.interpreter.spectrum.error_analysis()
110
111
112 self.interpreter.relax_fit.select_model('exp')
113
114
115 self.interpreter.grid_search(inc=self.grid_inc)
116
117
118 self.interpreter.minimise('simplex', scaling=False, constraints=False)
119
120
121 self.interpreter.monte_carlo.setup(number=self.mc_sim_num)
122 self.interpreter.monte_carlo.create_data()
123 self.interpreter.monte_carlo.initial_values()
124 self.interpreter.minimise('simplex', scaling=False, constraints=False)
125 self.interpreter.monte_carlo.error_analysis()
126
127
128 self.interpreter.value.write(param='rx', file=self.file_root+'.out', dir=self.results_dir, force=True)
129
130
131 self.interpreter.results.write(file='results', dir=self.results_dir, force=True)
132
133
134 self.interpreter.grace.write(y_data_type='chi2', file='chi2.agr', dir=self.grace_dir, force=True)
135 self.interpreter.grace.write(y_data_type='i0', file='i0.agr', dir=self.grace_dir, force=True)
136 self.interpreter.grace.write(y_data_type='rx', file=self.file_root+'.agr', dir=self.grace_dir, force=True)
137 self.interpreter.grace.write(x_data_type='relax_times', y_data_type='intensities', file='intensities.agr', dir=self.grace_dir, force=True)
138 self.interpreter.grace.write(x_data_type='relax_times', y_data_type='intensities', norm=True, file='intensities_norm.agr', dir=self.grace_dir, force=True)
139
140
141 if self.view_plots:
142 self.interpreter.grace.view(file='chi2.agr', dir=self.grace_dir)
143 self.interpreter.grace.view(file='i0.agr', dir=self.grace_dir)
144 self.interpreter.grace.view(file=self.file_root+'.agr', dir=self.grace_dir)
145 self.interpreter.grace.view(file='intensities.agr', dir=self.grace_dir)
146 self.interpreter.grace.view(file='intensities_norm.agr', dir=self.grace_dir)
147
148
149 self.interpreter.state.save(state=self.file_root+'.save', dir=self.results_dir, force=True)
150
151
153 """Check that the user has set the variables correctly."""
154
155
156 if not has_pipe(self.pipe_name):
157 raise RelaxNoPipeError(self.pipe_name)
158