Source Code for Module diffpy.srrietveld.utility

  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:    Peng Tian 
  9  # 
 10  # See AUTHORS.txt for a list of people who contributed. 
 11  # See LICENSE.txt for license information. 
 12  # 
 13  ################################################################################ 
 14   
 15  """Common shared functions that do not fit anywhere else. 
 16  """ 
 17   
 18  import os 
 19  import sys 
 20  import traceback 
 21  from hashlib import md5 
 22   
 23   
 24 -def checkFormat(filename): 
 25      """ Check the format of input file """ 
 26      filebasename = os.path.basename(filename) 
 27      fileformat = os.path.splitext(filebasename)[-1][1:].lower() 
 28      return fileformat 
 29   
 30   
 31 -def importClass(modpath, modname, classname, *args): 
 32      """ Import certain class with certain inputs """ 
 33      mod = __import__(modpath, globals(), locals(), [modname], -1) 
 34      cls = getattr(mod, classname) 
 35      return cls(*args) 
 36   
 37 -def parseXYToList(filename): 
 38      """ Parse XY or XYSigma data to list """ 
 39      # 1. read file 
 40      ifile = open(filename, "r") 
 41      inlines = ifile.readlines() 
 42      ifile.close() 
 43   
 44      # 2. parse content 
 45      datalist = [] 
 46      for line in inlines: 
 47          terms = line.strip().split() 
 48          if len(terms) > 1 and terms[0] not in ["#", ""]: 
 49              datalist.append((float(terms[0]), float(terms[1]))) 
 50      return datalist 
 51   
 52   
 53  # PJ FIXME: use the Python logging module instead 
 54   
 55 -def printWarning(warningMsg): 
 56      '''Print a red warning message to the std output 
 57      warningMsg : the warning message to be printed 
 58      ''' 
 59      #print '\\033[1;31m' + 'WARNING: ' + warningMsg + '\\033[1;m' 
 60      print 'WARNING: ' + warningMsg 
 61      return 
 62   
 63   
 64 -def unique(seq): 
 65      '''Get unique items from a sequence while keeping its original order''' 
 66      seen = set() 
 67      for item in seq: 
 68          if item in seen:  continue 
 69          seen.add(item) 
 70          yield item 
 71      pass 
 72   
 73   
 74 -def getFileid(fullpath): 
 75      '''get the md5 id of the file path 
 76      fullpath - the abs path of the file 
 77      return - the file path''' 
 78      fid = None 
 79      fid = md5(open(fullpath, 'rb').read()).hexdigest() 
 80      return fid 
 81   
 82   
 83 -def printDebugInfo(): 
 84      '''Print the information for debug''' 
 85      exc_type, exc_value, exc_traceback = sys.exc_info() 
 86      traceback.print_exception(exc_type, exc_value, exc_traceback, 
 87            limit=100, file=sys.stdout) 
 88      return 
 89   
 90  ############################################################################## 
 91  # csv reader and writer for unicode data, an extra encoding parameter is added 
 92  ############################################################################## 
 93   
 94  import csv, codecs, cStringIO 
 95   
 96 -class UTF8Recoder: 
 97      """ 
 98      Iterator that reads an encoded stream and reencodes the input to UTF-8 
 99      """ 
100 -    def __init__(self, f, encoding): 
101          self.reader = codecs.getreader(encoding)(f) 
102   
103 -    def __iter__(self): 
104          return self 
105   
106 -    def next(self): 
107          return self.reader.next().encode("utf-8") 
108   
109 -class UnicodeReader: 
110      """ 
111      A CSV reader which will iterate over lines in the CSV file "f", 
112      which is encoded in the given encoding. 
113      """ 
114   
115 -    def __init__(self, f, dialect=csv.excel, encoding="utf-8", **kwds): 
116          f = UTF8Recoder(f, encoding) 
117          self.reader = csv.reader(f, dialect=dialect, **kwds) 
118   
119 -    def next(self): 
120          row = self.reader.next() 
121          return [unicode(s, "utf-8") for s in row] 
122   
123 -    def __iter__(self): 
124          return self 
125   
126 -class UnicodeWriter: 
127      """ 
128      A CSV writer which will write rows to CSV file "f", 
129      which is encoded in the given encoding. 
130      """ 
131   
132 -    def __init__(self, f, dialect=csv.excel, encoding="utf-8", **kwds): 
133          # Redirect output to a queue 
134          self.queue = cStringIO.StringIO() 
135          self.writer = csv.writer(self.queue, dialect=dialect, **kwds) 
136          self.stream = f 
137          self.encoder = codecs.getincrementalencoder(encoding)() 
138   
139 -    def writerow(self, row): 
140          self.writer.writerow([s.encode("utf-8") for s in row]) 
141          # Fetch UTF-8 output from the queue ... 
142          data = self.queue.getvalue() 
143          data = data.decode("utf-8") 
144          # ... and reencode it into the target encoding 
145          data = self.encoder.encode(data) 
146          # write to the target stream 
147          self.stream.write(data) 
148          # empty queue 
149          self.queue.truncate(0) 
150   
151 -    def writerows(self, rows): 
152          for row in rows: 
153              self.writerow(row) 
154