Source Code for Module ComboCode.cc.tools.readers.SpectroscopyReader

  1  # -*- coding: utf-8 -*- 
  2   
  3  """ 
  4  A tool set for reading spectroscopy transition-based data. 
  5   
  6  Author: R. Lombaert 
  7   
  8  """ 
  9   
 10  import numpy as np, collections 
 11   
 12  from cc.tools.io import DataIO 
 13  from cc.tools.readers.Reader import Reader 
 14  from cc.data import Data 
 15   
 16   
 17 -class SpectroscopyReader(Reader): 
 18       
 19      '''  
 20      The SpectroscopyReader class. 
 21       
 22      Inherits from the Reader class, and thus functions much like a  
 23      dictionary.  
 24       
 25      SpectroscopyReader functions primarily as an intermediary class between  
 26      Reader and MolReader/CollisReader, both classes that make heavy use of  
 27      transition based indexing, and does relate to upper and lower level indices. 
 28           
 29      Typically not used stand-alone. Refer to MolReader and CollisReader for 
 30      practical uses. Both classes make use of this parent class' methods. 
 31       
 32      ''' 
 33       
 34 -    def __init__(self,fn,*args,**kwargs): 
 35           
 36          '''  
 37          Initialize an SpectroscopyReader object. 
 38           
 39          Additional args & kwargs passed to __init__ are passed to dict __init__.  
 40           
 41          @param fn: The filename of the file that is being read.  
 42          @type fn: str 
 43           
 44          ''' 
 45           
 46          #-- Create the dictionary instance  
 47          super(SpectroscopyReader,self).__init__(fn,*args,**kwargs) 
 48           
 49       
 50       
 51 -    def get(self,ptype,prop,index=None): 
 52       
 53          ''' 
 54          Return a property for a given type of property possibly for a given  
 55          index.  
 56           
 57          In case a single value is requested via index, the property value is 
 58          extracted from the array. 
 59           
 60          @param ptype: The type of property. 'coll_trans', 'trans' or 'level'. 
 61          @type ptype: str 
 62          @param prop: The property itself. eg 'energy' for level, or 'lup' for  
 63                       trans, or 'rates' for coll_trans. 
 64          @type prop: str 
 65           
 66          @keyword index: The index. In case of default, all are returned. Can be 
 67                          any array-like object that includes indices 
 68                           
 69                          (default: None) 
 70          @type index: int/array 
 71           
 72          @return: The property sorted by property type index, or a single element 
 73          @rtype: float/int/array 
 74           
 75          ''' 
 76           
 77          #-- Return all if no index specified, otherwise set an iterable. 
 78          if index is None: 
 79              return self[ptype][prop] 
 80               
 81          #-- Prefer explicit selection on indexing. Using indexing instead of  
 82          #   np.in1d to maintain the original shape of index. Assumes indexing in 
 83          #   files goes 1 -> i_max. This is normally the case. Much faster.  
 84          #selection = self[ptype][prop][np.in1d(self[ptype]['index'],index)] 
 85          selection = self[ptype][prop][Data.arrayify(index)-1] 
 86           
 87          #-- If a non-iterable object was passed as index, return just one value 
 88          #   if only one value was indeed found. Otherwise, just return as is. 
 89          if selection.shape != (1,) or isinstance(index,collections.Iterable): 
 90              return selection 
 91          else: 
 92              return selection[0] 
 93           
 94       
 95       
 96 -    def getTI(self,itype,lup=None,llow=None): 
 97           
 98          ''' 
 99          Return the indices of the transitions read from the molecular  
100          spectroscopy data or from the collisional rate data. 
101           
102          A specific index (or array of indices) can be requested by specifying  
103          the lower and upper level index. 
104           
105          Multiple lup and/or llow can be given in one go to make a selection of  
106          indices. 
107   
108          @param itype: The type of index. MolReader needs this to be 'trans'. 
109                        CollisReader needs this to be 'coll_trans'. 
110          @type itype: str 
111           
112          @keyword lup: The index of the upper energy level in the transition. If 
113                        both this and llow are None, all transition indices are  
114                        returned. 
115           
116                        (default: None) 
117          @type lup: int/array 
118          @keyword llow: The index of the lower energy level in the transition. If 
119                         both this and lup are None, all transition indices are  
120                         returned. 
121           
122                         (default: None) 
123          @type llow: int/array 
124           
125          @return: The transition indices. A single integer if both lup and llow 
126                   were single integers. 
127          @rtype: int/array 
128           
129          ''' 
130           
131          #-- Return all if no index given 
132          if lup is None and llow is None:  
133              return self[itype]['index'] 
134           
135          #-- Check for matches for given lup and llow. Will be empty array if no 
136          #   match found. 
137          bools = np.ones(shape=self[itype]['index'].shape,dtype=bool) 
138          if not lup is None:  
139              bools *= np.in1d(self[itype]['lup'],lup) 
140              #self[itype]['lup'] == lup 
141          if not llow is None: 
142              bools *= np.in1d(self[itype]['llow'],llow) 
143              #self[itype]['llow'] == llow 
144          selection = self[itype]['index'][bools] 
145           
146          #-- If both lup and llow were defined, only one index should be returned 
147          #   at least if only one index was found. Else return the entire array 
148          if selection.shape != (1,) or isinstance(lup,collections.Iterable) \ 
149                  or isinstance(llow,collections.Iterable): 
150              return selection 
151          else: 
152              return selection[0] 
153       
154       
155       
156 -    def getTUpper(self,index=None,itype='trans'): 
157           
158          ''' 
159          Return the indices of the upper states of the <nline> included  
160          transitions. 
161           
162          These are NOT the quantum numbers! Especially for CO-type molecules,  
163          the J-level is equal to level_index-1. 
164           
165          In case a single upper level is requested via index, the level index is 
166          extracted from the array. 
167   
168          @keyword index: The index. In case of default, all are returned. Can be 
169                          any array-like object that includes indices 
170                           
171                          (default: None) 
172          @type index: int/array 
173          @keyword itype: The type of index. Default is for MolReader.  
174                          CollisReader needs this to be 'coll_trans'. 
175                           
176                          (default: 'trans') 
177          @type itype: str 
178                   
179          @return: The upper level indices/x ordered by transition index. 
180          @rtype: array 
181           
182          ''' 
183           
184          return self.get(itype,'lup',index) 
185           
186       
187       
188 -    def getTLower(self,index=None,itype='trans'): 
189       
190          ''' 
191          Return the indices of the lower states of the <nline> included  
192          transitions. 
193           
194          These are NOT the quantum numbers! Especially for CO-type molecules,  
195          the J-level is equal to level_index-1. 
196   
197          In case a single lower level is requested via index, the level index is 
198          extracted from the array. 
199           
200          @keyword index: The index. In case of default, all are returned. Can be 
201                          any array-like object that includes indices 
202                           
203                          (default: None) 
204          @type index: int/array 
205          @keyword itype: The type of index. Default is for MolReader.  
206                          CollisReader needs this to be 'coll_trans'. 
207                           
208                          (default: 'trans') 
209          @type itype: str 
210                   
211          @return: The lower level indices/x ordered by transition index. 
212          @rtype: array 
213           
214          ''' 
215           
216          return self.get(itype,'llow',index) 
217