Source Code for Module fabio.openimage

  1  """ 
  2   
  3  Authors: Henning O. Sorensen & Erik Knudsen 
  4           Center for Fundamental Research: Metal Structures in Four Dimensions 
  5           Risoe National Laboratory 
  6           Frederiksborgvej 399 
  7           DK-4000 Roskilde 
  8           email:henning.sorensen@risoe.dk 
  9   
 10  mods for fabio by JPW 
 11   
 12  """ 
 13  import sys, logging 
 14  from fabioutils  import deconstruct_filename, getnum, filename_object 
 15  from fabioimage import fabioimage 
 16  import edfimage 
 17  import adscimage 
 18  import tifimage 
 19  import marccdimage 
 20  import mar345image 
 21  import fit2dmaskimage 
 22  import brukerimage 
 23  import bruker100image 
 24  import pnmimage 
 25  import GEimage 
 26  import OXDimage 
 27  import dm3image 
 28  import HiPiCimage 
 29  import pilatusimage 
 30  import fit2dspreadsheetimage 
 31  import kcdimage 
 32  import cbfimage 
 33  import xsdimage 
 34   
 35  MAGIC_NUMBERS = [ 
 36      # "\42\5a" : 'bzipped' 
 37      # "\1f\8b" : 'gzipped' 
 38      ("FORMAT :        86" , 'bruker'), 
 39      ("\x4d\x4d\x00\x2a"   , 'tif') , 
 40      # The marCCD and Pilatus formats are both standard tif with a header 
 41      # hopefully these byte patterns are unique for the formats 
 42      # If not the image will be read, but the is missing  
 43      ("\x49\x49\x2a\x00\x08\x00"   , 'marccd') , 
 44      ("\x49\x49\x2a\x00\x82\x00"   , 'pilatus') , 
 45      ("\x49\x49\x2a\x00"   , 'tif') , 
 46      # ADSC must come before edf 
 47      ("{\nHEA"             , 'adsc'), 
 48      ("{"                  , 'edf'), 
 49      ("\r{"                , 'edf'), 
 50      ("\n{"                , 'edf'), 
 51      ("ADEPT"              , 'GE'), 
 52      ("OD"                 , 'OXD'), 
 53      ("IM"                 , 'HiPiC'), 
 54      ('\x2d\x04'           , 'mar345'), 
 55      ('\x04\x2d'           , 'mar345'), #some machines may need byteswapping 
 56      # hint : MASK in 32 bit 
 57      ('M\x00\x00\x00A\x00\x00\x00S\x00\x00\x00K\x00\x00\x00' , 'fit2dmask') , 
 58      ('\x00\x00\x00\x03'   , 'dm3'), 
 59      ("No"                 , "kcd"), 
 60      ("<"                  , "xsd") 
 61      ] 
 62   
 63 -def do_magic(byts): 
 64      """ Try to interpret the bytes starting the file as a magic number """ 
 65      for magic, format in MAGIC_NUMBERS: 
 66          if byts.find(magic) == 0: 
 67              return format 
 68          if 0: # debugging - bruker needed 18 bytes below 
 69              print "m:", magic, "f:", format, 
 70              print "bytes:", magic, "len(bytes)", len(magic), 
 71              print "found:", byts.find(magic) 
 72              for i in range(len(magic)): 
 73                  print ord(magic[i]), ord(byts[i]), magic[i], byts[i] 
 74      raise Exception("Could not interpret magic string") 
 75   
 76   
 77 -def openimage(filename): 
 78      """ Try to open an image """ 
 79      if isinstance(filename, filename_object): 
 80          try: 
 81              obj = _openimage(filename.tostring()) 
 82              obj.read(filename.tostring()) 
 83          except: 
 84              # multiframe file 
 85              #print "DEBUG: multiframe file, start # %d"%( 
 86              #    filename.num) 
 87              obj = _openimage(filename.stem) 
 88              obj.read(filename.stem, frame=filename.num) 
 89      else: 
 90          obj = _openimage(filename) 
 91          obj.read(filename) 
 92      return obj 
 93   
 94   
 95 -def openheader(filename): 
 96      """ return only the header""" 
 97      obj = _openimage(filename) 
 98      obj.readheader(filename) 
 99      return obj 
100   
101   
102 -def _openimage(filename): 
103      """  
104      determine which format for a filename 
105      and return appropriate class which can be used for opening the image 
106      """ 
107      try: 
108          imo = fabioimage() 
109          byts = imo._open(filename).read(18) 
110          filetype = do_magic(byts) 
111          # print filetype 
112          if filetype == "marccd" and filename.find("mccd") == -1: 
113              # Cannot see a way around this. Need to find something 
114              # to distinguish mccd from regular tif... 
115              filetype = "tif" 
116          #UNUSED filenumber = getnum(filename) 
117      except IOError: 
118          # File probably does not exist 
119          raise 
120      except: 
121          try: 
122              file_obj = deconstruct_filename(filename) 
123              if file_obj == None: 
124                  raise Exception 
125              if len(file_obj.format) != 1 and \ 
126                      type(file_obj.format) != type(["list"]): 
127                  # one of OXD/ ADSC - should have got in previous 
128                  raise Exception("openimage failed on magic bytes & name guess") 
129              filetype = file_obj.format 
130              #UNUSED filenumber = file_obj.num 
131          except: 
132              #import traceback 
133              #traceback.print_exc() 
134              raise Exception("Fabio could not identify " + filename) 
135      klass_name = "".join(filetype) + 'image' 
136  #    print "looking for %s in" % klass_name 
137  #    for i in sys.modules: 
138  #        if klass_name in i: 
139  #            print "%s\t%s" % (i, sys.modules[i]) 
140      module = sys.modules.get("fabio." + klass_name, None) 
141  #    if hasattr(__init__, klass_name): 
142  #        module = getattr(__init__, klass_name) 
143      if module is not None: 
144          if hasattr(module, klass_name): 
145              klass = getattr(module, klass_name) 
146                  # print klass 
147          else: 
148              raise Exception("Module %s has no image class" % module) 
149      else: 
150          raise Exception("Filetype not known %s %s" % (filename, klass_name)) 
151      obj = klass() 
152      # skip the read for read header 
153      return obj 
154