Source Code for Module gui.components.spectrum

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2009-2011 Michael Bieri                                       # 
  4  # Copyright (C) 2010-2013 Edward d'Auvergne                                   # 
  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.                                         # 
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 13  # This program is distributed in the hope that it will be useful,             # 
 14  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
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 16  # GNU General Public License for more details.                                # 
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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 containing the classes for GUI components involving spectral data.""" 
 25   
 26  # Python module imports. 
 27  import wx 
 28  import wx.lib.buttons 
 29   
 30  # relax module imports. 
 31  from graphics import fetch_icon 
 32  from gui.components.base_list import Base_list 
 33  from gui.string_conv import float_to_gui, gui_to_str, str_to_gui 
 34  from gui.uf_objects import Uf_storage; uf_store = Uf_storage() 
 35  from pipe_control.spectrum import replicated_flags, replicated_ids 
 36  from status import Status; status = Status() 
 37  from user_functions.data import Uf_info; uf_info = Uf_info() 
 38   
 39   
 40 -class Spectra_list(Base_list): 
 41      """The GUI element for listing loaded spectral data.""" 
 42   
 43 -    def __init__(self, gui=None, parent=None, box=None, id=None, fn_add=None, proportion=0, button_placement='default', relax_times=False): 
 44          """Build the spectral list GUI element. 
 45   
 46          @keyword gui:               The main GUI object. 
 47          @type gui:                  wx.Frame instance 
 48          @keyword parent:            The parent GUI element that this is to be attached to (the panel object). 
 49          @type parent:               wx object 
 50          @keyword data:              The data storage container. 
 51          @type data:                 class instance 
 52          @keyword box:               The vertical box sizer to pack this GUI component into. 
 53          @type box:                  wx.BoxSizer instance 
 54          @keyword id:                A unique identification string.  This is used to register the update method with the GUI user function observer object. 
 55          @type id:                   str 
 56          @keyword fn_add:            The function to execute when clicking on the 'Add' button. 
 57          @type fn_add:               func 
 58          @keyword proportion:        The window proportion parameter. 
 59          @type proportion:           bool 
 60          @keyword button_placement:  Override the button visibility and placement.  The value of 'default' will leave the buttons at the default setting.  The value of 'top' will place the buttons at the top, 'bottom' will place them at the bottom, and None will turn off the buttons. 
 61          @type button_placement:     str or None 
 62          @keyword relax_times:       A flag which if True will activate the relaxation time parts of the GUI element. 
 63          @type relax_times:          bool 
 64          """ 
 65   
 66          # Store the arguments. 
 67          self.fn_add = fn_add 
 68          self.relax_times_flag = relax_times 
 69   
 70          # Initialise the base class. 
 71          super(Spectra_list, self).__init__(gui=gui, parent=parent, box=box, id=id, proportion=proportion, button_placement=button_placement) 
 72   
 73   
 74 -    def action_relax_fit_relax_time(self, event): 
 75          """Launch the relax_fit.relax_time user function. 
 76   
 77          @param event:   The wx event. 
 78          @type event:    wx event 
 79          """ 
 80   
 81          # The current selection. 
 82          item = self.element.GetFirstSelected() 
 83   
 84          # The spectrum ID. 
 85          id = gui_to_str(self.element.GetItemText(item)) 
 86   
 87          # The current time. 
 88          time = None 
 89          if hasattr(cdp, 'relax_times') and id in cdp.relax_times.keys(): 
 90              time = cdp.relax_times[id] 
 91   
 92          # Launch the dialog. 
 93          if time == None: 
 94              uf_store['relax_fit.relax_time'](spectrum_id=id) 
 95          else: 
 96              uf_store['relax_fit.relax_time'](time=time, spectrum_id=id) 
 97   
 98   
 99 -    def action_spectrum_baseplane_rmsd(self, event): 
100          """Launch the spectrum.baseplane_rmsd user function. 
101   
102          @param event:   The wx event. 
103          @type event:    wx event 
104          """ 
105   
106          # The current selection. 
107          item = self.element.GetFirstSelected() 
108   
109          # The spectrum ID. 
110          id = gui_to_str(self.element.GetItemText(item)) 
111   
112          # Launch the dialog. 
113          uf_store['spectrum.baseplane_rmsd'](spectrum_id=id) 
114   
115   
116 -    def action_spectrum_delete(self, event): 
117          """Launch the spectrum.delete user function. 
118   
119          @param event:   The wx event. 
120          @type event:    wx event 
121          """ 
122   
123          # The current selection. 
124          item = self.element.GetFirstSelected() 
125   
126          # No selection. 
127          if item == -1: 
128              id = None 
129   
130          # Selected item. 
131          else: 
132              # The spectrum ID. 
133              id = gui_to_str(self.element.GetItemText(item)) 
134   
135          # Launch the dialog. 
136          uf_store['spectrum.delete'](spectrum_id=id) 
137   
138   
139 -    def action_spectrum_integration_points(self, event): 
140          """Launch the spectrum.integration_points user function. 
141   
142          @param event:   The wx event. 
143          @type event:    wx event 
144          """ 
145   
146          # The current selection. 
147          item = self.element.GetFirstSelected() 
148   
149          # The spectrum ID. 
150          id = gui_to_str(self.element.GetItemText(item)) 
151   
152          # Launch the dialog. 
153          uf_store['spectrum.integration_points'](spectrum_id=id) 
154   
155   
156 -    def action_spectrum_replicated(self, event): 
157          """Launch the spectrum.replicated user function. 
158   
159          @param event:   The wx event. 
160          @type event:    wx event 
161          """ 
162   
163          # The current selection. 
164          item = self.element.GetFirstSelected() 
165   
166          # The spectrum ID. 
167          id = gui_to_str(self.element.GetItemText(item)) 
168   
169          # The current replicates. 
170          replicates = replicated_ids(id) 
171   
172          # Launch the dialog. 
173          if replicates == []: 
174              uf_store['spectrum.replicated'](spectrum_ids=id) 
175          else: 
176              uf_store['spectrum.replicated'](spectrum_ids=replicates) 
177   
178   
179 -    def noe_spectrum_type(self, index): 
180          """Add the NOE spectral type info to the element. 
181   
182          @param index:   The column index for the data. 
183          @type index:    int 
184          @return:        True if a spectrum type exists, False otherwise. 
185          @rtype:         bool 
186          """ 
187   
188          # No type info. 
189          if not hasattr(cdp, 'spectrum_type') or not len(cdp.spectrum_type): 
190              return False 
191   
192          # Append a column. 
193          self.element.InsertColumn(index, str_to_gui("NOE spectrum type")) 
194   
195          # Translation table. 
196          table = { 
197              'sat': 'Saturated', 
198              'ref': 'Reference' 
199          } 
200   
201          # Set the values. 
202          for i in range(len(cdp.spectrum_ids)): 
203              # No value. 
204              if cdp.spectrum_ids[i] not in cdp.spectrum_type.keys(): 
205                  continue 
206   
207              # Set the value. 
208              self.element.SetStringItem(i, index, str_to_gui(table[cdp.spectrum_type[cdp.spectrum_ids[i]]])) 
209   
210          # Successful. 
211          return True 
212   
213   
214 -    def relax_times(self, index): 
215          """Add the relaxation delay time info to the element. 
216   
217          @param index:   The column index for the data. 
218          @type index:    int 
219          @return:        True if relaxation times exist, False otherwise. 
220          @rtype:         bool 
221          """ 
222   
223          # No type info. 
224          if not hasattr(cdp, 'relax_times') or not len(cdp.relax_times): 
225              return False 
226   
227          # Append a column. 
228          self.element.InsertColumn(index, str_to_gui("Delay times (s)")) 
229   
230          # Set the values. 
231          for i in range(len(cdp.spectrum_ids)): 
232              # No value. 
233              if cdp.spectrum_ids[i] not in cdp.relax_times.keys(): 
234                  continue 
235   
236              # Set the value. 
237              self.element.SetStringItem(i, index, float_to_gui(cdp.relax_times[cdp.spectrum_ids[i]])) 
238   
239          # Successful. 
240          return True 
241   
242   
243 -    def replicates(self, index): 
244          """Add the replicated spectra info to the element. 
245   
246          @param index:   The column index for the data. 
247          @type index:    int 
248          @return:        True if relaxation times exist, False otherwise. 
249          @rtype:         bool 
250          """ 
251   
252          # No type info. 
253          if not hasattr(cdp, 'replicates') or not len(cdp.replicates): 
254              return False 
255   
256          # Replicated spectra. 
257          repl = replicated_flags() 
258   
259          # Append a column. 
260          self.element.InsertColumn(index, str_to_gui("Replicate IDs")) 
261   
262          # Set the values. 
263          for i in range(len(cdp.spectrum_ids)): 
264              # No replicates. 
265              if not repl[cdp.spectrum_ids[i]]: 
266                  continue 
267   
268              # The replicated spectra. 
269              id_list = replicated_ids(cdp.spectrum_ids[i]) 
270   
271              # Convert to a string. 
272              text = '' 
273              for j in range(len(id_list)): 
274                  # Add the id. 
275                  text = "%s%s" % (text, id_list[j]) 
276   
277                  # Separator. 
278                  if j < len(id_list)-1: 
279                      text = "%s, " % text 
280   
281              # Set the value. 
282              self.element.SetStringItem(i, index, str_to_gui(text)) 
283   
284          # Successful. 
285          return True 
286   
287   
288 -    def setup(self): 
289          """Override the base variables.""" 
290   
291          # GUI variables. 
292          self.title = "Spectra list" 
293          self.observer_base_name = "spectra list" 
294   
295          # The column titles. 
296          self.columns = [] 
297   
298          # Button set up. 
299          self.button_placement = 'top' 
300          self.button_info = [ 
301              { 
302                  'object': 'button_add', 
303                  'label': ' Add', 
304                  'icon': fetch_icon('oxygen.actions.list-add-relax-blue', "22x22"), 
305                  'method': self.fn_add, 
306                  'tooltip': "Read a spectral data file." 
307              }, { 
308                  'object': 'button_delete', 
309                  'label': ' Delete', 
310                  'icon': fetch_icon('oxygen.actions.list-remove', "22x22"), 
311                  'method': self.action_spectrum_delete, 
312                  'tooltip': "Delete loaded relaxation data from the relax data store." 
313              } 
314          ] 
315   
316          # The right click popup menu. 
317          self.popup_menus = [ 
318              { 
319                  'id': wx.NewId(), 
320                  'text': "Set the &baseplane RMSD", 
321                  'icon': fetch_icon(uf_info.get_uf('spectrum.baseplane_rmsd').gui_icon), 
322                  'method': self.action_spectrum_baseplane_rmsd 
323              }, { 
324                  'id': wx.NewId(), 
325                  'text': "&Delete the peak intensities", 
326                  'icon': fetch_icon(uf_info.get_uf('spectrum.delete').gui_icon), 
327                  'method': self.action_spectrum_delete 
328              }, { 
329                  'id': wx.NewId(), 
330                  'text': "Set the number of integration &points", 
331                  'icon': fetch_icon(uf_info.get_uf('spectrum.integration_points').gui_icon), 
332                  'method': self.action_spectrum_integration_points 
333              }, { 
334                  'id': wx.NewId(), 
335                  'text': "Specify which spectra are &replicated", 
336                  'icon': fetch_icon(uf_info.get_uf('spectrum.replicated').gui_icon), 
337                  'method': self.action_spectrum_replicated 
338              } 
339          ] 
340          if self.relax_times_flag: 
341              self.popup_menus.append({ 
342                  'id': wx.NewId(), 
343                  'text': "Set the relaxation &time", 
344                  'icon': fetch_icon(uf_info.get_uf('relax_fit.relax_time').gui_icon), 
345                  'method': self.action_relax_fit_relax_time 
346              }) 
347   
348   
349 -    def update_data(self): 
350          """Method called from self.build_element_safe() to update the list data.""" 
351   
352          # Initialise the column index for the data. 
353          index = 1 
354   
355          # Delete the rows and columns. 
356          self.element.DeleteAllItems() 
357          self.element.DeleteAllColumns() 
358   
359          # Initialise to a single column. 
360          self.element.InsertColumn(0, str_to_gui("Spectrum ID")) 
361   
362          # Expand the number of rows to match the number of spectrum IDs, and add the IDs. 
363          n = 0 
364          if hasattr(cdp, 'spectrum_ids'): 
365              # The number of IDs. 
366              n = len(cdp.spectrum_ids) 
367   
368              # Set the IDs. 
369              for i in range(n): 
370                  self.element.InsertStringItem(i, str_to_gui(cdp.spectrum_ids[i])) 
371   
372          # The NOE spectrum type. 
373          if self.noe_spectrum_type(index): 
374              index += 1 
375   
376          # The relaxation times. 
377          if self.relax_times_flag and self.relax_times(index): 
378              index += 1 
379   
380          # The replicated spectra. 
381          if self.replicates(index): 
382              index += 1 
383