Source Code for Module fabio.adscimage

  1   
  2  ## Automatically adapted for numpy.oldnumeric Oct 05, 2007 by alter_code1.py 
  3   
  4  #!/usr/bin/env python 
  5  """ 
  6   
  7  Authors: Henning O. Sorensen & Erik Knudsen 
  8           Center for Fundamental Research: Metal Structures in Four Dimensions 
  9           Risoe National Laboratory 
 10           Frederiksborgvej 399 
 11           DK-4000 Roskilde 
 12           email:erik.knudsen@risoe.dk 
 13   
 14  + mods for fabio by JPW 
 15   
 16  """ 
 17   
 18  import numpy as N, logging 
 19  from fabioimage import fabioimage 
 20   
 21   
 22 -class adscimage(fabioimage): 
 23      """ Read an image in ADSC format (quite similar to edf?) """ 
 24   
 25 -    def read(self, fname): 
 26          """ read in the file """ 
 27          infile = self._open(fname, "rb") 
 28          try: 
 29              self._readheader(infile) 
 30          except: 
 31              raise Exception("Error processing adsc header") 
 32          # banned by bzip/gzip??? 
 33          try: 
 34              infile.seek(int(self.header['HEADER_BYTES']), 0) 
 35          except TypeError: 
 36              # Gzipped does not allow a seek and read header is not 
 37              # promising to stop in the right place 
 38              infile.close() 
 39              infile = self._open(fname, "rb") 
 40              infile.read(int(self.header['HEADER_BYTES'])) 
 41          binary = infile.read() 
 42          infile.close() 
 43   
 44          #now read the data into the array 
 45          self.dim1 = int(self.header['SIZE1']) 
 46          self.dim2 = int(self.header['SIZE2']) 
 47          if 'little' in self.header['BYTE_ORDER']: 
 48              try: 
 49                  self.data = N.reshape( 
 50                      N.fromstring(binary, N.uint16), 
 51                      (self.dim2, self.dim1)) 
 52              except ValueError: 
 53                  raise IOError, 'Size spec in ADSC-header does not match ' + \ 
 54                      'size of image data field' 
 55              self.bytecode = N.uint16 
 56              logging.info("adscimage read in using low byte first (x386-order)") 
 57          else: 
 58              try: 
 59                  self.data = N.reshape( 
 60                      N.fromstring(binary, N.uint16), 
 61                      (self.dim2, self.dim1)).byteswap() 
 62              except ValueError: 
 63                  raise IOError, 'Size spec in ADSC-header does not match ' + \ 
 64                      'size of image data field' 
 65              self.bytecode = N.uint16 
 66              logging.info('adscimage using high byte first (network order)') 
 67          self.resetvals() 
 68          return self 
 69   
 70   
 71 -    def _readheader(self, infile): 
 72          """ read an adsc header """ 
 73          line = infile.readline() 
 74          bytesread = len(line) 
 75          while '}' not in line: 
 76              if '=' in line: 
 77                  (key, val) = line.split('=') 
 78                  self.header_keys.append(key.strip()) 
 79                  self.header[key.strip()] = val.strip(' ;\n') 
 80              line = infile.readline() 
 81              bytesread = bytesread + len(line) 
 82   
 83   
 84 -    def write(self, fname): 
 85          """ 
 86          Write adsc format 
 87          """ 
 88          out = '{\n' 
 89          for key in self.header_keys: 
 90              out += "%s = %s;\n" % (key, self.header[key]) 
 91          # FIXME ??? - made padding match header bytes keyword             
 92          #        the cbflib example image has exactly 512... 
 93          if self.header.has_key("HEADER_BYTES"): 
 94              pad = int(self.header["HEADER_BYTES"]) - len(out) - 2 
 95          else: 
 96              # integer division 
 97              # 1234567890123456789012 
 98              # HEADER_BYTES = 1234;\n 
 99              hsize = ((len(out) + 23) / 512 + 1) * 512 
100              out += "HEADER_BYTES=%d;\n" % (hsize) 
101              pad = hsize - len(out) - 2 
102          out += pad * ' ' + "}\n" 
103          assert len(out) % 512 == 0 , "Header is not multiple of 512" 
104          outf = open(fname, "wb") 
105          outf.write(out) 
106          # it says "unsigned_short" ? ... jpw example has: 
107          # BYTE_ORDER=big_endian; 
108          # TYPE=unsigned_short; 
109          if "little" in self.header["BYTE_ORDER"]: 
110              outf.write(self.data.astype(N.uint16).tostring()) 
111          else: 
112              outf.write(self.data.byteswap().astype( 
113                      N.uint16).tostring()) 
114          outf.close() 
115   
116   
117 -def test(): 
118      """ testcase """ 
119      import sys, time 
120      img = adscimage() 
121      begin = time.clock() 
122      while (sys.argv[1:]): 
123          img.read(sys.argv[1]) 
124  #        rim = img.toPIL16() 
125          img.rebin(2, 2) 
126          img.write('jegErEnFil0000.img') 
127          print sys.argv[1] + ": max=%d, min=%d, mean=%.2e, stddev=%.2e" % (\ 
128                img.getmax(), img.getmin(), img.getmean(), img.getstddev()) 
129          print 'integrated intensity (%d %d %d %d) =%.3f' % (\ 
130                10, 20, 20, 40, img.integrate_area((10, 20, 20, 40))) 
131          sys.argv[1:] = sys.argv[2:] 
132      end = time.clock() 
133      print end - begin 
134   
135   
136  if __name__ == '__main__': 
137      test() 
138