Source Code for Module fabio.HiPiCimage

  1   
  2  #!/usr/bin/env python 
  3  """ 
  4  Authors: Henning O. Sorensen & Erik Knudsen 
  5           Center for Fundamental Research: Metal Structures in Four Dimensions 
  6           Risoe National Laboratory 
  7           Frederiksborgvej 399 
  8           DK-4000 Roskilde 
  9           email:erik.knudsen@risoe.dk 
 10   
 11          + Jon Wright, ESRF 
 12   
 13  Information about the file format from Masakatzu Kobayashi is highly appreciated 
 14  """ 
 15   
 16  import numpy as np, logging 
 17   
 18  from fabioimage import fabioimage 
 19   
 20 -class HiPiCimage(fabioimage): 
 21      """ Read HiPic images e.g. collected with a Hamamatsu CCD camera""" 
 22   
 23   
 24 -    def _readheader(self, infile): 
 25          """ 
 26          Read in a header from an already open file 
 27   
 28          """ 
 29          Image_tag = infile.read(2) 
 30          print Image_tag 
 31          Comment_len = np.fromstring(infile.read(2), np.uint16) 
 32          Dim_1 = np.fromstring(infile.read(2), np.uint16)[0] 
 33          Dim_2 = np.fromstring(infile.read(2), np.uint16)[0] 
 34          Dim_1_offset = np.fromstring(infile.read(2), np.uint16)[0] 
 35          Dim_2_offset = np.fromstring(infile.read(2), np.uint16)[0] 
 36          HeaderType = np.fromstring(infile.read(2), np.uint16)[0] 
 37          Dump = infile.read(50) 
 38          Comment = infile.read(Comment_len) 
 39          self.header['Image_tag'] = Image_tag 
 40          self.header['Dim_1'] = Dim_1 
 41          self.header['Dim_2'] = Dim_2 
 42          self.header['Dim_1_offset'] = Dim_1_offset 
 43          self.header['Dim_2_offset'] = Dim_2_offset 
 44          #self.header['Comment'] = Comment 
 45          if Image_tag != 'IM' : 
 46              # This does not look like an HiPic file 
 47              logging.warning("no opening.  Corrupt header of HiPic file " + \ 
 48                              str(infile.name)) 
 49          Comment_split = Comment[:Comment.find('\x00')].split('\r\n') 
 50   
 51          for topcomment in Comment_split: 
 52              topsplit = topcomment.split(',') 
 53              for line in topsplit: 
 54                  if '=' in line: 
 55                      key, val = line.split('=' , 1) 
 56                      # Users cannot type in significant whitespace 
 57                      key = key.rstrip().lstrip() 
 58                      self.header_keys.append(key) 
 59                      self.header[key] = val.lstrip().rstrip() 
 60                      self.header[key] = val.lstrip('"').rstrip('"') 
 61   
 62 -    def read(self, fname): 
 63          """ 
 64          Read in header into self.header and 
 65              the data   into self.data 
 66          """ 
 67          self.header = {} 
 68          self.resetvals() 
 69          infile = self._open(fname, "rb") 
 70          self._readheader(infile) 
 71          # Compute image size 
 72          try: 
 73              self.dim1 = int(self.header['Dim_1']) 
 74              self.dim2 = int(self.header['Dim_2']) 
 75          except: 
 76              raise Exception("HiPic file", str(fname) + \ 
 77                                  "is corrupt, cannot read it") 
 78          bytecode = np.uint16 
 79          self.bpp = len(np.array(0, bytecode).tostring()) 
 80   
 81          # Read image data 
 82          block = infile.read(self.dim1 * self.dim2 * self.bpp) 
 83          infile.close() 
 84   
 85          #now read the data into the array 
 86          try: 
 87              self.data = np.reshape( 
 88                  np.fromstring(block, bytecode), 
 89                  [self.dim2, self.dim1]) 
 90          except: 
 91              print len(block), bytecode, self.bpp, self.dim2, self.dim1 
 92              raise IOError, \ 
 93                'Size spec in HiPic-header does not match size of image data field' 
 94          self.bytecode = self.data.dtype.type 
 95   
 96          # Sometimes these files are not saved as 12 bit, 
 97          # But as 16 bit after bg subtraction - which results  
 98          # negative values saved as 16bit. Therefore values higher  
 99          # 4095 is really negative values 
100          if self.data.max() > 4095: 
101              gt12bit = self.data > 4095 
102              self.data = self.data - gt12bit * (2 ** 16 - 1) 
103   
104          # ensure the PIL image is reset 
105          self.pilimage = None 
106          return self 
107