Source Code for Module specific_analyses.relax_disp.checks

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2013 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).          # 
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 10  # the Free Software Foundation, either version 3 of the License, or           # 
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 13  # This program is distributed in the hope that it will be useful,             # 
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 16  # GNU General Public License for more details.                                # 
 17  #                                                                             # 
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 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.dispersion.variables import EXP_TYPE_LIST_CPMG, EXP_TYPE_LIST_R1RHO, MODEL_LIST_R1RHO_OFF_RES, MODEL_NOREX 
 32  from lib.errors import RelaxError, RelaxFuncSetupError, RelaxNoPeakIntensityError 
 33  import specific_analyses 
 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: 
 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: 
 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: 
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_interpolate_offset_cpmg_model(interpolate=None): 
118      """Check interpolating through offsets in CPMG models. 
119   
120      @keyword interpolate:           How to interpolate the fitted curves.  Either by option "%s" which interpolate CPMG frequency or spin-lock field strength, or by option "%s" which interpole over spin-lock offset. 
121      @type interpolate:              str 
122      @raises RelaxFuncSetupError:    If the interpolate method is set to 'offset' for not-R1rho models. 
123      """%(specific_analyses.relax_disp.data.INTERPOLATE_DISP, specific_analyses.relax_disp.data.INTERPOLATE_OFFSET) 
124   
125      # Check if interpolating against offset for CPMG models. 
126      # This is currently not implemented, and will raise an error. 
127      if not specific_analyses.relax_disp.data.has_r1rho_exp_type() and interpolate == specific_analyses.relax_disp.data.INTERPOLATE_OFFSET: 
128          raise RelaxFuncSetupError("interpolating against Spin-lock offset for CPMG models") 
129   
130   
131 -def check_mixed_curve_types(): 
132      """Prevent both fixed time and exponential curves from being analysed simultaneously. 
133   
134      @raises RelaxError: If mixed curve types are present. 
135      """ 
136   
137      # No experiment types set. 
138      if not hasattr(cdp, 'exp_type') or not hasattr(cdp, 'spectrum_ids') or not hasattr(cdp, 'relax_times'): 
139          return False 
140   
141      # Get the times. 
142      times = get_times() 
143   
144      # Loop over all experiment types. 
145      var_flag = False 
146      fixed_flag = False 
147      for exp_type in times: 
148          if times[exp_type] == 1: 
149              fixed_flag = True 
150          else: 
151              var_flag = True 
152   
153      # The check. 
154      if var_flag and fixed_flag: 
155          raise RelaxError("Fixed time and exponential curves cannot be analysed simultaneously.") 
156   
157   
158 -def check_model_type(model=None): 
159      """Check that the dispersion model has been set. 
160   
161      @keyword model:     The model which to select. 
162      @type model:        str 
163      @raises RelaxError: If the dispersion model has not been specified. 
164      """ 
165   
166      # Test if the model has been set. 
167      if not hasattr(cdp, 'model_type'): 
168          if model != None: 
169              text = "The relaxation dispersion model '%s' has not been specified.  Set by: relax_disp.select_model('%s')." % (model, model) 
170          else: 
171              text = "The relaxation dispersion model has not been specified." 
172          raise RelaxError(text) 
173   
174   
175 -def check_pipe_type(): 
176      """Check that the data pipe type is that of relaxation dispersion. 
177   
178      @raises RelaxFuncSetupError:    If the data pipe type is not set to 'relax_disp'. 
179      """ 
180   
181      # Test if the pipe type is set to 'relax_disp'. 
182      function_type = cdp.pipe_type 
183      if function_type != 'relax_disp': 
184          raise RelaxFuncSetupError(specific_analyses.setup.get_string(function_type)) 
185   
186   
187 -def check_missing_r1(model=None): 
188      """Check if R1 data is missing for the model. 
189   
190      @keyword model: The model to test for. 
191      @type model:    str 
192      @return:        Return True if R1 data is not available for the model. 
193      @rtype:         bool 
194      """ 
195   
196      # Check that the model uses R1 data. 
197      if model in [MODEL_NOREX] + MODEL_LIST_R1RHO_OFF_RES: 
198          # If R1 ids are present. 
199          if hasattr(cdp, 'ri_ids'): 
200              return False 
201   
202          # If not present. 
203          else: 
204              return True 
205   
206      # If model does not need R1. 
207      else: 
208          return False 
209   
210   
211 -def check_relax_times(): 
212      """Check if the spectrometer frequencies have been set up. 
213   
214      @raises RelaxError: If the spectrometer frequencies have not been set. 
215      """ 
216   
217      # Test if the experiment type is set. 
218      if not hasattr(cdp, 'relax_times'): 
219          raise RelaxError("The relaxation times have not been set for any spectra.") 
220   
221      # Check each spectrum ID. 
222      for id in cdp.exp_type: 
223          if id not in cdp.relax_times: 
224              raise RelaxError("The relaxation time has not been set for the '%s' spectrum." % id) 
225   
226   
227 -def check_spectra_id_setup(): 
228      """Check that the data for each spectra ID is correctly set up. 
229   
230      This is an alias for the following checks: 
231   
232          - check_spectrum_ids() 
233          - check_exp_type() 
234          - check_spectrometer_frq() 
235          - check_disp_points() 
236          - check_relax_times() 
237   
238   
239      @raises RelaxError: If data is missing. 
240      """ 
241   
242      # Perform the checks. 
243      check_spectrum_ids() 
244      check_exp_type() 
245      check_spectrometer_frq() 
246      check_disp_points() 
247      check_relax_times() 
248   
249   
250 -def check_spectrometer_frq(): 
251      """Check if the spectrometer frequencies have been set up. 
252   
253      @raises RelaxError: If the spectrometer frequencies have not been set. 
254      """ 
255   
256      # Test if the experiment type is set. 
257      if not hasattr(cdp, 'spectrometer_frq'): 
258          raise RelaxError("The spectrometer frequencies have not been set for any spectra.") 
259   
260      # Check each spectrum ID. 
261      for id in cdp.exp_type: 
262          if id not in cdp.spectrometer_frq: 
263              raise RelaxError("The spectrometer frequency has not been set for the '%s' spectrum." % id) 
264   
265   
266 -def check_spectrum_ids(): 
267      """Check if spectrum IDs exist. 
268   
269      @raises RelaxNoPeakIntensityError:  If no spectrum IDs exist. 
270      """ 
271   
272      # The spectrum IDs structure. 
273      if not hasattr(cdp, 'spectrum_ids') or len(cdp.spectrum_ids) == 0: 
274          raise RelaxNoPeakIntensityError 
275   
276   
277 -def get_times(): 
278      """Create a per-experiment dictionary of relaxation times. 
279       
280      @return:    The dictionary of unique relaxation times. 
281      @rtype:     dict of float 
282      """ 
283   
284      # Initialise. 
285      times = {} 
286      for type in cdp.exp_type_list: 
287          times[type] = [] 
288   
289      # Not set up yet. 
290      if not hasattr(cdp, 'exp_type') or not hasattr(cdp, 'spectrum_ids') or not hasattr(cdp, 'relax_times'): 
291          return times 
292   
293      # Loop over all spectra IDs. 
294      for id in cdp.exp_type: 
295          # No time set. 
296          if id not in cdp.relax_times: 
297              continue 
298   
299          # No type set. 
300          if id not in cdp.exp_type: 
301              continue 
302   
303          # Count the number of times. 
304          if cdp.relax_times[id] not in times[cdp.exp_type[id]]: 
305              times[cdp.exp_type[id]].append(cdp.relax_times[id]) 
306   
307      # Return the times dictionary. 
308      return times 
309