Source Code for Module specific_analyses.relax_fit.parameter_object

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2002-2014 Edward d'Auvergne                                   # 
  4  # Copyright (C) 2006 Chris MacRaild                                           # 
  5  # Copyright (C) 2007-2008 Sebastien Morin                                     # 
  6  #                                                                             # 
  7  # This file is part of the program relax (http://www.nmr-relax.com).          # 
  8  #                                                                             # 
  9  # This program is free software: you can redistribute it and/or modify        # 
 10  # it under the terms of the GNU General Public License as published by        # 
 11  # the Free Software Foundation, either version 3 of the License, or           # 
 12  # (at your option) any later version.                                         # 
 13  #                                                                             # 
 14  # This program is distributed in the hope that it will be useful,             # 
 15  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
 16  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
 17  # GNU General Public License for more details.                                # 
 18  #                                                                             # 
 19  # You should have received a copy of the GNU General Public License           # 
 20  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 21  #                                                                             # 
 22  ############################################################################### 
 23   
 24  # Module docstring. 
 25  """The module for the relaxation curve fitting parameter list object.""" 
 26   
 27  # Python module imports. 
 28  from numpy import average 
 29   
 30  # relax module imports. 
 31  from lib.mathematics import round_to_next_order 
 32  from specific_analyses.parameter_object import Param_list 
 33   
 34   
 35 -def i_scaling(model_info=None): 
 36      """Determine the scaling factor for the peak intensities. 
 37   
 38      This is for the scaling of the I0 and Iinf parameters during optimisation.  The maximum intensity will be used to scale all values. 
 39   
 40   
 41      @keyword model_info:    The spin container and the spin ID string from the _model_loop_spin() specific API method. 
 42      @type model_info:       SpinContainer instance, str 
 43      @return:                The average peak intensity of the first time point. 
 44      @rtype:                 float 
 45      """ 
 46   
 47      # Unpack the data. 
 48      spin, spin_id = model_info 
 49   
 50      # The scaling factor as the maximum intensity. 
 51      return round_to_next_order(max(spin.peak_intensity.values())) 
 52   
 53   
 54 -def i0_upper(incs=None, model_info=None): 
 55      """Find the upper bound for the I0 parameter. 
 56   
 57      @keyword incs:          The number of grid search increments. 
 58      @type incs:             int 
 59      @keyword model_info:    The spin container and the spin ID string from the _model_loop_spin() specific API method. 
 60      @type model_info:       SpinContainer instance, str 
 61      @return:                The average peak intensity of the first time point. 
 62      @rtype:                 float 
 63      """ 
 64   
 65      # Unpack the data. 
 66      spin, spin_id = model_info 
 67   
 68      # Find the maximum intensity. 
 69      upper = max(spin.peak_intensity.values()) 
 70   
 71      # Multiply the value by 2.0 and then round up to the next order - this will be the upper bound. 
 72      return round_to_next_order(upper * 2.0) 
 73   
 74   
 75 -def iinf_upper(incs=None, model_info=None): 
 76      """Find the average intensity of the last time point. 
 77   
 78      This is for the grid search upper bound for the Iinf parameter. 
 79   
 80   
 81      @keyword incs:          The number of grid search increments. 
 82      @type incs:             int 
 83      @keyword model_info:    The spin container and the spin ID string from the _model_loop_spin() specific API method. 
 84      @type model_info:       SpinContainer instance, str 
 85      @return:                The average peak intensity of the last time point. 
 86      @rtype:                 float 
 87      """ 
 88   
 89      # Unpack the data. 
 90      spin, spin_id = model_info 
 91   
 92      # Find the ID of the last time point. 
 93      max_time = max(cdp.relax_times.values()) 
 94      for key in cdp.relax_times: 
 95          if cdp.relax_times[key] == max_time: 
 96              id = key 
 97              break 
 98   
 99      # The averaged value. 
100      upper = average(spin.peak_intensity[id]) 
101   
102      # Multiply the value by 2.0 and then round up to the next order - this will be the upper bound. 
103      return round_to_next_order(upper * 2.0) 
104   
105   
106   
107 -class Relax_fit_params(Param_list): 
108      """The relaxation curve fitting parameter list singleton.""" 
109   
110      # Class variable for storing the class instance (for the singleton design pattern). 
111      _instance = None 
112   
113 -    def __init__(self): 
114          """Define all the parameters of the analysis.""" 
115   
116          # The object is already initialised. 
117          if self._initialised: return 
118   
119          # Execute the base class __init__() method. 
120          Param_list.__init__(self) 
121   
122          # Add the base data. 
123          self._add_peak_intensity() 
124   
125          # Add the signal to noise ratio. 
126          self._add_sn_ratio() 
127   
128          # Add the base information for the analysis. 
129          self._add( 
130              'relax_times', 
131              scope = 'spin', 
132              py_type = dict, 
133              grace_string = '\\qRelaxation time period (s)\\Q' 
134          ) 
135   
136          # Add the model variables. 
137          self._add_model_info(model_flag=False) 
138   
139          # Add the model parameters. 
140          self._add( 
141              'rx', 
142              scope = 'spin', 
143              default = 8.0, 
144              units = 'rad.s^-1', 
145              desc = 'Either the R1 or R2 relaxation rate', 
146              set = 'params', 
147              py_type = float, 
148              scaling = 1.0, 
149              grid_lower = 0.0, 
150              grid_upper = 20.0, 
151              grace_string = '\\qR\\sx\\Q', 
152              grace_units = 'rad.s\\S-1\\N', 
153              err = True, 
154              sim = True 
155          ) 
156          self._add( 
157              'i0', 
158              scope = 'spin', 
159              default = 10000.0, 
160              desc = 'The initial intensity', 
161              py_type = float, 
162              set = 'params', 
163              scaling = i_scaling, 
164              grid_lower = 0.0, 
165              grid_upper = i0_upper, 
166              grace_string = '\\qI\\s0\\Q', 
167              err = True, 
168              sim = True 
169          ) 
170          self._add( 
171              'iinf', 
172              scope = 'spin', 
173              default = 0.0, 
174              desc = 'The intensity at infinity', 
175              py_type = float, 
176              set = 'params', 
177              scaling = i_scaling, 
178              grid_lower = 0.0, 
179              grid_upper = iinf_upper, 
180              grace_string = '\\qI\\sinf\\Q', 
181              err = True, 
182              sim = True 
183          ) 
184   
185          # Add the minimisation data. 
186          self._add_min_data(min_stats_global=False, min_stats_spin=True) 
187   
188          # Set up the user function documentation. 
189          self._set_uf_title("Relaxation curve fitting parameters") 
190          self._uf_param_table(label="table: curve-fit parameters", caption="Relaxation curve fitting parameters.") 
191          self._uf_param_table(label="table: curve-fit parameters and min stats", caption="Relaxation curve fitting parameters and minimisation statistics.", sets=['params', 'fixed', 'min']) 
192          self._uf_param_table(label="table: curve-fit parameter value setting", caption="Relaxation curve fitting parameters.") 
193          self._uf_param_table(label="table: curve-fit parameter value setting with defaults", caption="Relaxation curve fitting parameter value setting.", default=True) 
194