Source Code for Module specific_analyses.relax_disp.checks

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2013 Edward d'Auvergne                                        # 
  4  # Copyright (C) 2013-2014 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  """Module for functions for checking different aspects of the dispersion setup. 
 25   
 26  These functions raise various RelaxErrors to help the user understand what went wrong.  To avoid circular imports, these functions must be independent and not import anything from the specific_analyses.relax_disp package (the variables module is an exception). 
 27  """ 
 28   
 29  # relax module imports. 
 30  from dep_check import C_module_exp_fn 
 31  from lib.errors import RelaxError, RelaxFuncSetupError, RelaxNoPeakIntensityError 
 32  import specific_analyses 
 33  from specific_analyses.relax_disp.variables import EXP_TYPE_LIST_CPMG, EXP_TYPE_LIST_R1RHO 
 34   
 35   
 36 -def check_c_modules(): 
 37      """Check for the presence of the compiled C-modules. 
 38   
 39      @raises RelaxError: If the compiled C-module is not present and exponential curves are required. 
 40      """ 
 41   
 42      # Get the times. 
 43      times = get_times() 
 44   
 45      # Complain. 
 46      for exp_type in times: 
 47          if len(times[exp_type]) > 1 and not C_module_exp_fn: 
 48              raise RelaxError("The exponential curve-fitting C module cannot be found.") 
 49   
 50   
 51 -def check_disp_points(): 
 52      """Check that the CPMG frequencies or spin-lock field strengths have been set up. 
 53   
 54      @raises RelaxError: If the dispersion point data is missing. 
 55      """ 
 56   
 57      # Test if the curve count exists. 
 58      if not hasattr(cdp, 'dispersion_points'): 
 59          raise RelaxError("The CPMG frequencies or spin-lock field strengths have not been set for any spectra.") 
 60   
 61      # Check each spectrum ID. 
 62      for id in cdp.exp_type.keys(): 
 63          # CPMG data. 
 64          if cdp.exp_type[id] in EXP_TYPE_LIST_CPMG: 
 65              if id not in cdp.cpmg_frqs: 
 66                  raise RelaxError("The nu_CPMG frequency has not been set for the '%s' spectrum." % id) 
 67   
 68          # R1rho data. 
 69          elif cdp.exp_type[id] in EXP_TYPE_LIST_R1RHO: 
 70              if id not in cdp.spin_lock_nu1: 
 71                  raise RelaxError("The spin-lock field strength has not been set for the '%s' spectrum." % id) 
 72   
 73   
 74 -def check_exp_type(id=None): 
 75      """Check if the experiment type have been set up for one or all IDs. 
 76   
 77      @param id:          The experiment ID string.  If not set, then all spectrum IDs will be checked. 
 78      @type id:           None or str 
 79      @raises RelaxError: When the experiment type for the given ID is missing or, when not given, if the dispersion experiment type has not been set. 
 80      """ 
 81   
 82      # Test if the experiment type is set. 
 83      if not hasattr(cdp, 'exp_type'): 
 84          raise RelaxError("The relaxation dispersion experiment types have not been set for any spectra.") 
 85   
 86      # Individual ID. 
 87      if id != None: 
 88          if id not in cdp.exp_type.keys(): 
 89              raise RelaxError("The dispersion experiment type for the experiment ID '%s' has not been set." % id) 
 90   
 91      # Check that at least one spectrum ID is set. 
 92      else: 
 93          found = False 
 94          for id in cdp.spectrum_ids: 
 95              if id in cdp.exp_type: 
 96                  found = True 
 97          if not found: 
 98              raise RelaxError("The relaxation dispersion experiment type has not been set any spectra.") 
 99   
100   
101 -def check_exp_type_fixed_time(): 
102      """Check that only fixed time experiment types have been set up. 
103   
104      @raises RelaxError: If exponential curves are present. 
105      """ 
106   
107      # Loop over the id's. 
108      for id in cdp.exp_type.keys(): 
109          # Get the exp_type and frq. 
110          exp_type = cdp.exp_type[id] 
111          frq = cdp.spectrometer_frq[id] 
112   
113          if specific_analyses.relax_disp.data.count_relax_times(exp_type = exp_type, frq = frq, ei = cdp.exp_type_list.index(cdp.exp_type[id])) > 1: 
114              raise RelaxError("The experiment '%s' is not of the fixed relaxation time period data type." % exp_type) 
115   
116   
117 -def check_mixed_curve_types(): 
118      """Prevent both fixed time and exponential curves from being analysed simultaneously. 
119   
120      @raises RelaxError: If mixed curve types are present. 
121      """ 
122   
123      # No experiment types set. 
124      if not hasattr(cdp, 'exp_type') or not hasattr(cdp, 'spectrum_ids') or not hasattr(cdp, 'relax_times'): 
125          return False 
126   
127      # Get the times. 
128      times = get_times() 
129   
130      # Loop over all experiment types. 
131      var_flag = False 
132      fixed_flag = False 
133      for exp_type in times: 
134          if times[exp_type] == 1: 
135              fixed_flag = True 
136          else: 
137              var_flag = True 
138   
139      # The check. 
140      if var_flag and fixed_flag: 
141          raise RelaxError("Fixed time and exponential curves cannot be analysed simultaneously.") 
142   
143   
144 -def check_model_type(): 
145      """Check that the dispersion model has been set. 
146   
147      @raises RelaxError: If the dispersion model has not been specified. 
148      """ 
149   
150      # Test if the model has been set. 
151      if not hasattr(cdp, 'model_type'): 
152          raise RelaxError("The relaxation dispersion model has not been specified.") 
153   
154   
155 -def check_pipe_type(): 
156      """Check that the data pipe type is that of relaxation dispersion. 
157   
158      @raises RelaxFuncSetupError:    If the data pipe type is not set to 'relax_disp'. 
159      """ 
160   
161      # Test if the pipe type is set to 'relax_disp'. 
162      function_type = cdp.pipe_type 
163      if function_type != 'relax_disp': 
164          raise RelaxFuncSetupError(specific_analyses.setup.get_string(function_type)) 
165   
166   
167 -def check_relax_times(): 
168      """Check if the spectrometer frequencies have been set up. 
169   
170      @raises RelaxError: If the spectrometer frequencies have not been set. 
171      """ 
172   
173      # Test if the experiment type is set. 
174      if not hasattr(cdp, 'relax_times'): 
175          raise RelaxError("The relaxation times have not been set for any spectra.") 
176   
177      # Check each spectrum ID. 
178      for id in cdp.exp_type.keys(): 
179          if id not in cdp.relax_times: 
180              raise RelaxError("The relaxation time has not been set for the '%s' spectrum." % id) 
181   
182   
183 -def check_spectra_id_setup(): 
184      """Check that the data for each spectra ID is correctly set up. 
185   
186      This is an alias for the following checks: 
187   
188          - check_spectrum_ids() 
189          - check_exp_type() 
190          - check_spectrometer_frq() 
191          - check_disp_points() 
192          - check_relax_times() 
193   
194   
195      @raises RelaxError: If data is missing. 
196      """ 
197   
198      # Perform the checks. 
199      check_spectrum_ids() 
200      check_exp_type() 
201      check_spectrometer_frq() 
202      check_disp_points() 
203      check_relax_times() 
204   
205   
206 -def check_spectrometer_frq(): 
207      """Check if the spectrometer frequencies have been set up. 
208   
209      @raises RelaxError: If the spectrometer frequencies have not been set. 
210      """ 
211   
212      # Test if the experiment type is set. 
213      if not hasattr(cdp, 'spectrometer_frq'): 
214          raise RelaxError("The spectrometer frequencies have not been set for any spectra.") 
215   
216      # Check each spectrum ID. 
217      for id in cdp.exp_type.keys(): 
218          if id not in cdp.spectrometer_frq: 
219              raise RelaxError("The spectrometer frequency has not been set for the '%s' spectrum." % id) 
220   
221   
222 -def check_spectrum_ids(): 
223      """Check if spectrum IDs exist. 
224   
225      @raises RelaxNoPeakIntensityError:  If no spectrum IDs exist. 
226      """ 
227   
228      # The spectrum IDs structure. 
229      if not hasattr(cdp, 'spectrum_ids') or len(cdp.spectrum_ids) == 0: 
230          raise RelaxNoPeakIntensityError 
231   
232   
233 -def get_times(): 
234      """Create a per-experiment dictionary of relaxation times. 
235       
236      @return:    The dictionary of unique relaxation times. 
237      @rtype:     dict of float 
238      """ 
239   
240      # Initialise. 
241      times = {} 
242      for type in cdp.exp_type_list: 
243          times[type] = [] 
244   
245      # Not set up yet. 
246      if not hasattr(cdp, 'exp_type') or not hasattr(cdp, 'spectrum_ids') or not hasattr(cdp, 'relax_times'): 
247          return times 
248   
249      # Loop over all spectra IDs. 
250      for id in cdp.exp_type.keys(): 
251          # No time set. 
252          if id not in cdp.relax_times: 
253              continue 
254   
255          # No type set. 
256          if id not in cdp.exp_type: 
257              continue 
258   
259          # Count the number of times. 
260          if cdp.relax_times[id] not in times[cdp.exp_type[id]]: 
261              times[cdp.exp_type[id]].append(cdp.relax_times[id]) 
262   
263      # Return the times dictionary. 
264      return times 
265