Source Code for Module user_functions.relax_fit

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2004-2015 Edward d'Auvergne                                   # 
  4  # Copyright (C) 2014 Troels E. Linnet                                         # 
  5  #                                                                             # 
  6  # This file is part of the program relax (http://www.nmr-relax.com).          # 
  7  #                                                                             # 
  8  # This program is free software: you can redistribute it and/or modify        # 
  9  # it under the terms of the GNU General Public License as published by        # 
 10  # the Free Software Foundation, either version 3 of the License, or           # 
 11  # (at your option) any later version.                                         # 
 12  #                                                                             # 
 13  # This program is distributed in the hope that it will be useful,             # 
 14  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
 15  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
 16  # GNU General Public License for more details.                                # 
 17  #                                                                             # 
 18  # You should have received a copy of the GNU General Public License           # 
 19  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 20  #                                                                             # 
 21  ############################################################################### 
 22   
 23  # Module docstring. 
 24  """The relax_fit user function definitions.""" 
 25   
 26  # relax module imports. 
 27  from graphics import ANALYSIS_IMAGE_PATH 
 28  from lib.text.gui import i0, iinf, rx 
 29  from pipe_control import spectrum 
 30  from specific_analyses.relax_fit.uf import relax_time, select_model 
 31  from user_functions.data import Uf_info; uf_info = Uf_info() 
 32  from user_functions.objects import Desc_container 
 33   
 34   
 35  # The user function class. 
 36  uf_class = uf_info.add_class('relax_fit') 
 37  uf_class.title = "Class for relaxation curve fitting." 
 38  uf_class.menu_text = "&relax_fit" 
 39  uf_class.gui_icon = "relax.relax_fit" 
 40   
 41   
 42  # The relax_fit.relax_time user function. 
 43  uf = uf_info.add_uf('relax_fit.relax_time') 
 44  uf.title = "Set the relaxation delay time associated with each spectrum." 
 45  uf.title_short = "Relaxation delay time setting." 
 46  uf.add_keyarg( 
 47      name = "time", 
 48      default = 0.0, 
 49      py_type = "num", 
 50      desc_short = "relaxation time", 
 51      desc = "The time, in seconds, of the relaxation period." 
 52  ) 
 53  uf.add_keyarg( 
 54      name = "spectrum_id", 
 55      py_type = "str", 
 56      desc_short = "spectrum identification string", 
 57      desc = "The spectrum identification string.", 
 58      wiz_element_type = 'combo', 
 59      wiz_combo_iter = spectrum.get_ids, 
 60      wiz_read_only = True 
 61  ) 
 62  # Description. 
 63  uf.desc.append(Desc_container()) 
 64  uf.desc[-1].add_paragraph("Peak intensities should be loaded before calling this user function via the spectrum.read_intensities user function.  The intensity values will then be associated with a spectrum identifier.  To associate each spectrum identifier with a time point in the relaxation curve prior to optimisation, this user function should be called.") 
 65  uf.backend = relax_time 
 66  uf.menu_text = "&relax_time" 
 67  uf.gui_icon = "oxygen.actions.chronometer" 
 68  uf.wizard_size = (700, 500) 
 69  uf.wizard_image = ANALYSIS_IMAGE_PATH + 'r1_200x200.png' 
 70   
 71   
 72  # The relax_fit.select_model user function. 
 73  uf = uf_info.add_uf('relax_fit.select_model') 
 74  uf.title = "Select the relaxation curve type." 
 75  uf.title_short = "Relaxation curve type selection." 
 76  uf.display = True 
 77  uf.add_keyarg( 
 78      name = "model", 
 79      default = "exp", 
 80      py_type = "str", 
 81      desc_short = "model", 
 82      desc = "The type of relaxation curve to fit.", 
 83      wiz_element_type = "combo", 
 84      wiz_combo_choices = [ 
 85          "Two parameter exponential fit: [%s, %s]" % (rx, i0), 
 86          "Inversion recovery: [%s, %s, %s]" % (rx, i0, iinf), 
 87          "Saturation recovery: [%s, %s]" % (rx, iinf) 
 88      ], 
 89      wiz_combo_data = [ 
 90          "exp", 
 91          "inv", 
 92          "sat" 
 93      ], 
 94      wiz_read_only = True 
 95  ) 
 96  # Description. 
 97  uf.desc.append(Desc_container()) 
 98  uf.desc[-1].add_paragraph("A number of relaxation experiments are supported and include:") 
 99  uf.desc[-1].add_paragraph("The 'exp' model.  This is the default two parameter exponential fit.  The magnetisation starts at I0 and decays to zero.  The parameters are [Rx, I0] and the equation is I(t) = I0*exp(-Rx*t).") 
100  uf.desc[-1].add_paragraph("The 'inv' model.  This is the inversion recovery experiment (IR).  The magnetisation starts at a negative value at -I0 and relaxes to a positive Iinf value.  The parameters are [Rx, I0, Iinf] and the equation is I(t) = Iinf - I0*exp(-Rx*t).") 
101  uf.desc[-1].add_paragraph("The 'sat' model.  This is the saturation recovery experiment (SR).  The magnetisation starts at zero and relaxes to a positive Iinf value.  The parameters are [Rx, Iinf] and the equation is I(t) = Iinf*(1 - exp(-Rx*t)).") 
102  uf.backend = select_model 
103  uf.menu_text = "&select_model" 
104  uf.gui_icon = "oxygen.actions.list-add" 
105  uf.wizard_height_desc = 500 
106  uf.wizard_size = (900, 600) 
107  uf.wizard_apply_button = False 
108  uf.wizard_image = ANALYSIS_IMAGE_PATH + 'r1_200x200.png' 
109