Source Code for Module diffpy.srrietveld.convert.datafile

  1  ############################################################################## 
  2  # 
  3  # diffpy.srrietveld by DANSE Diffraction group 
  4  #                   Simon J. L. Billinge 
  5  #                   (c) 2009 Trustees of the Columbia University 
  6  #                   in the City of New York.  All rights reserved. 
  7  # 
  8  # File coded by:    Yingrui Shang 
  9  # 
 10  # See AUTHORS.txt for a list of people who contributed. 
 11  # See LICENSE.txt for license information. 
 12  # 
 13  ############################################################################## 
 14  '''Read the information from the data file. Currently an interface. Using the  
 15  functionality in addon/datafile.py, will improve later''' 
 16   
 17  __id__ = "$Id: datafile.py 6718 2011-08-23 21:33:20Z yshang $" 
 18   
 19  from diffpy.srrietveld.addon.datafile import DataFileConverter 
 20  from diffpy.srrietveld.exceptions import SrrFileError 
 21  import os 
 22   
 23 -class DataFile: 
 24      '''The data file class''' 
 25 -    def __init__(self, filepath = None, engine = None,  
 26                   xobs = None, yobs = None, ysig = None, rootname = None): 
 27          '''Constructor, the DataFile can be initiated either from a file path  
 28          or arrays of data 
 29          filepath - the filepath of the data file 
 30          engine - the engine type 
 31          xobs, yobs, ysig - the data arrays to initialize the data file 
 32          rootname - the rootname of the file when constructed from x/y data arrays.  
 33              NOTE: the extension name is always dat in this case''' 
 34           
 35          if filepath is not None: 
 36              if not os.path.exists(filepath): 
 37                  raise SrrFileError('The data file ' + filepath + ' does not exist.') 
 38                  if not os.path.isfile(filepath): 
 39                      raise SrrFileError('The data file path' + filepath + 'is not' + \ 
 40                                         'a path to a file. ') 
 41               
 42              self.engine = engine 
 43              self.filename = os.path.basename(filepath) 
 44              self.data = open(filepath, 'rb').read() 
 45               
 46              self.xobs = [] 
 47              self.yobs = [] 
 48              self.ysig = [] 
 49           
 50          if xobs is not None: 
 51              self.xobs = xobs 
 52              self.yobs = yobs 
 53              self.ysig = ysig 
 54               
 55              self.filename = 'datafile.dat' if rootname is None else rootname + '.dat'  
 56               
 57              # the length of the data is determined by xobs 
 58              line = [] 
 59              for idx, xx in enumerate(xobs): 
 60                  if self.ysig is not None: 
 61                      line.append("%s %s %s" %(xx, self.yobs[idx], self.ysig[idx])) 
 62                  else: 
 63                      line.append("%s %s" %(xx, self.yobs[idx])) 
 64               
 65              self.data = '\n'.join(line) 
 66               
 67          return 
 68       
 69 -    def __str__(self): 
 70          '''String conversion''' 
 71          return str(self.data) 
 72       
 73 -    def __isConversionNeeded(self): 
 74          '''Check if the file needs conversion 
 75          engine - gsas or fullprof 
 76          return - True if conversion is needed''' 
 77          engine = self.engine 
 78           
 79          root, ext = os.path.splitext(self.filename) 
 80          if engine.lower() == 'gsas': 
 81              if ext in [".chi", ".dat", ".txt", 'xye']: 
 82                  return True 
 83              elif ext in [".gsa", ".gda", "fxye", "raw"]: 
 84                  return False 
 85          if engine.lower() == 'fullprof': 
 86              if ext in [".chi", ".gsa", ".gda", "fxye", "raw"]: 
 87                  return True 
 88              elif ext in [".dat"]: 
 89                  return False 
 90          else: 
 91              from diffpy.srrietveld.utility import printWarning 
 92              __warningMsg = 'Data file extension is not recognized. The ' + \ 
 93                  'refinement may not run correctly. ' 
 94              printWarning(__warningMsg) 
 95           
 96          return False 
 97       
 98 -    def dump(self, directory, basename = None): 
 99          '''dump the file to the directory 
100          dir: the directory to dump the file 
101          rootname: the new file name, if not none will replace self.filename 
102          return the file path where the file dumped''' 
103          nm = self.filename if basename is None else basename 
104          filepath = os.path.join(directory, nm) 
105          with open(filepath, 'wb') as f: 
106              f.write(self.data) 
107          return filepath 
108       
109 -    def write(self, filepath): 
110          '''Write to filepath''' 
111          with open(filepath, 'wb') as f: 
112              f.write(self.data) 
113          return 
114   
115 -    def prepDataFile(self, newDir, instrumentFile = None, filename = None): 
116          '''Prepare the data file for different engines, and dump the prepared  
117          file to a path. If conversion is not needed, the origianl file will be  
118          dumped new directory - the path to dump the file 
119          engine - the engine 
120          rootName - the file name if different from that saved in the object 
121          return the path to the prepared data file''' 
122          from diffpy.srrietveld.addon.datafile import DataFileConverter 
123          from diffpy.srrietveld.utility import printWarning 
124           
125          if not instrumentFile: 
126              instrumentFile = None 
127           
128          fullpath = self.dump(newDir, filename) 
129   
130          root, ext = os.path.splitext(fullpath) 
131           
132          if filename: 
133              root = os.path.splitext(filename)[0] 
134               
135          newPath = fullpath 
136           
137          if self.__isConversionNeeded(): 
138              dataFile = DataFileConverter(fullpath) 
139              if self.engine.lower() == 'gsas': 
140                  newPath = root + '.gsa' 
141                  # bank id is always 1 
142                  dataFile.toGSASFile(fullpath, newPath, 1) 
143              if self.engine.lower() == 'fullprof': 
144                  newPath = root + '.dat' 
145                   
146                  if ext.lower() != '.chi': 
147                      __warningMsg = 'To convert GSAS data file, installation of ' + \ 
148                      'GSAS is needed and an instrument file is required. ' 
149                       
150                      printWarning(__warningMsg) 
151                  # FIXM: convert gsas data file name to fullprof data file name 
152                  # search the local directory for EXP files, may implement a  
153                  # better algrethm 
154                  dfc = DataFileConverter(fullpath, instrumentFile) 
155                  import glob 
156                  desfile = os.path.join(os.getcwd(), "*.EXP") 
157                  expfilename = None 
158                  for fn in glob.glob(desfile): 
159                      expfilename = fn 
160                  if expfilename: 
161                      dfc.toFPFile(fullpath, newPath, 1, expfilename) 
162                  elif ext.lower() == '.chi': 
163                      dfc.toFPFile(fullpath, newPath, 1) 
164                  else: 
165                      __warningMsg = "To convert GSAS data file, GSAS is needed " + \ 
166                      "to be installed and an instrument file is required." + \ 
167                      "The gsas data file can not be converted. The refinment may " + \ 
168                      "not run. " 
169                      printWarning(__warningMsg) 
170                       
171          return newPath 
172