Source Code for Module auto_analyses.relax_fit

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2004-2014 Edward d'Auvergne                                   # 
  4  #                                                                             # 
  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
  6  #                                                                             # 
  7  # This program is free software: you can redistribute it and/or modify        # 
  8  # it under the terms of the GNU General Public License as published by        # 
  9  # the Free Software Foundation, either version 3 of the License, or           # 
 10  # (at your option) any later version.                                         # 
 11  #                                                                             # 
 12  # This program is distributed in the hope that it will be useful,             # 
 13  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
 14  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
 15  # GNU General Public License for more details.                                # 
 16  #                                                                             # 
 17  # You should have received a copy of the GNU General Public License           # 
 18  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 19  #                                                                             # 
 20  ############################################################################### 
 21   
 22  # Module docstring. 
 23  """The automatic relaxation curve fitting protocol.""" 
 24   
 25  # Python module imports. 
 26  from os import sep 
 27   
 28  # relax module imports. 
 29  from pipe_control.pipes import cdp_name, has_pipe, switch 
 30  from prompt.interpreter import Interpreter 
 31  from status import Status; status = Status() 
 32   
 33   
 34   
 35 -class Relax_fit: 
 36 -    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): 
 37          """Perform relaxation curve fitting. 
 38   
 39          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: 
 40   
 41              - All the spins loaded. 
 42              - Unresolved spins deselected. 
 43              - All the peak intensities loaded and relaxation delay times set. 
 44              - Either the baseplane noise RMDS values should be set or replicated spectra loaded. 
 45   
 46          @keyword pipe_name:     The name of the data pipe containing all of the data for the analysis. 
 47          @type pipe_name:        str 
 48          @keyword pipe_bundle:   The data pipe bundle to associate all spawned data pipes with. 
 49          @type pipe_bundle:      str 
 50          @keyword file_root:     File root of the output filea. 
 51          @type file_root:        str 
 52          @keyword results_dir:   The directory where results files are saved. 
 53          @type results_dir:      str 
 54          @keyword grid_inc:      Number of grid search increments. 
 55          @type grid_inc:         int 
 56          @keyword mc_sim_num:    The number of Monte Carlo simulations to be used for error analysis at the end of the analysis. 
 57          @type mc_sim_num:       int 
 58          @keyword view_plots:    Flag to automatically view grace plots after calculation. 
 59          @type view_plots:       bool 
 60          """ 
 61   
 62          # Execution lock. 
 63          status.exec_lock.acquire(pipe_bundle, mode='auto-analysis') 
 64   
 65          # Set up the analysis status object. 
 66          status.init_auto_analysis(pipe_bundle, type='relax_fit') 
 67          status.current_analysis = pipe_bundle 
 68   
 69          # Store the args. 
 70          self.pipe_name = pipe_name 
 71          self.pipe_bundle = pipe_bundle 
 72          self.file_root = file_root 
 73          self.results_dir = results_dir 
 74          if self.results_dir: 
 75              self.grace_dir = results_dir + sep + 'grace' 
 76          else: 
 77              self.grace_dir = 'grace' 
 78          self.mc_sim_num = mc_sim_num 
 79          self.grid_inc = grid_inc 
 80          self.view_plots = view_plots 
 81   
 82          # Data checks. 
 83          self.check_vars() 
 84   
 85          # Set the data pipe to the current data pipe. 
 86          if self.pipe_name != cdp_name(): 
 87              switch(self.pipe_name) 
 88   
 89          # Load the interpreter. 
 90          self.interpreter = Interpreter(show_script=False, raise_relax_error=True) 
 91          self.interpreter.populate_self() 
 92          self.interpreter.on(verbose=False) 
 93   
 94          # Execute. 
 95          self.run() 
 96   
 97          # Finish and unlock execution. 
 98          status.auto_analysis[self.pipe_bundle].fin = True 
 99          status.current_analysis = None 
100          status.exec_lock.release() 
101   
102   
103 -    def run(self): 
104          """Set up and run the curve-fitting.""" 
105   
106          # Peak intensity error analysis. 
107          self.interpreter.spectrum.error_analysis() 
108   
109          # Set the relaxation curve type. 
110          self.interpreter.relax_fit.select_model('exp') 
111   
112          # Grid search. 
113          self.interpreter.grid_search(inc=self.grid_inc) 
114   
115          # Minimise. 
116          self.interpreter.minimise('simplex', scaling=False, constraints=False) 
117   
118          # Monte Carlo simulations. 
119          self.interpreter.monte_carlo.setup(number=self.mc_sim_num) 
120          self.interpreter.monte_carlo.create_data() 
121          self.interpreter.monte_carlo.initial_values() 
122          self.interpreter.minimise('simplex', scaling=False, constraints=False) 
123          self.interpreter.monte_carlo.error_analysis() 
124   
125          # Save the relaxation rates. 
126          self.interpreter.value.write(param='rx', file=self.file_root+'.out', dir=self.results_dir, force=True) 
127   
128          # Save the results. 
129          self.interpreter.results.write(file='results', dir=self.results_dir, force=True) 
130   
131          # Create Grace plots of the data. 
132          self.interpreter.grace.write(y_data_type='chi2', file='chi2.agr', dir=self.grace_dir, force=True)    # Minimised chi-squared value. 
133          self.interpreter.grace.write(y_data_type='i0', file='i0.agr', dir=self.grace_dir, force=True)    # Initial peak intensity. 
134          self.interpreter.grace.write(y_data_type='rx', file=self.file_root+'.agr', dir=self.grace_dir, force=True)    # Relaxation rate. 
135          self.interpreter.grace.write(x_data_type='relax_times', y_data_type='peak_intensity', file='intensities.agr', dir=self.grace_dir, force=True)    # Average peak intensities. 
136          self.interpreter.grace.write(x_data_type='relax_times', y_data_type='peak_intensity', norm=True, file='intensities_norm.agr', dir=self.grace_dir, force=True)    # Average peak intensities (normalised). 
137   
138          # Display the Grace plots if selected. 
139          if self.view_plots: 
140              self.interpreter.grace.view(file='chi2.agr', dir=self.grace_dir) 
141              self.interpreter.grace.view(file='i0.agr', dir=self.grace_dir) 
142              self.interpreter.grace.view(file=self.file_root+'.agr', dir=self.grace_dir) 
143              self.interpreter.grace.view(file='intensities.agr', dir=self.grace_dir) 
144              self.interpreter.grace.view(file='intensities_norm.agr', dir=self.grace_dir) 
145   
146          # Save the program state. 
147          self.interpreter.state.save(state=self.file_root+'.save', dir=self.results_dir, force=True) 
148   
149   
150 -    def check_vars(self): 
151          """Check that the user has set the variables correctly.""" 
152   
153          # The pipe name. 
154          if not has_pipe(self.pipe_name): 
155              raise RelaxNoPipeError(self.pipe_name) 
156