Source Code for Module fabio.mar345image

  1  #!/usr/bin/env python 
  2  """ 
  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, France 
 12  """ 
 13   
 14  from fabioimage import fabioimage 
 15  import numpy, struct, string 
 16   
 17 -class mar345image(fabioimage): 
 18      _need_a_real_file = True 
 19 -    def read(self, fname): 
 20          """ Read a mar345 image""" 
 21          self.filename = fname 
 22          f = self._open(self.filename, "rb") 
 23          self._readheader(f) 
 24   
 25          try: 
 26              import mar345_io 
 27          except: 
 28              print 'error importing the mar345_io backend - ' + \ 
 29                  'generating empty 1x1 picture' 
 30              f.close() 
 31              self.dim1 = 1 
 32              self.dim2 = 1 
 33              self.bytecode = numpy.int # 
 34              self.data = numpy.resize(numpy.array([0], numpy.int), [1, 1]) 
 35              return self 
 36   
 37          if 'compressed' in self.header['Format']: 
 38              self.data = mar345_io.unpack(f, self.dim1, self.dim2, self.numhigh) 
 39          else: 
 40              print "error: cannot handle these formats yet " + \ 
 41                  "due to lack of documentation" 
 42              return None 
 43          self.bytecode = numpy.uint 
 44          f.close() 
 45          return self 
 46   
 47 -    def _readheader(self, infile=None): 
 48          """ Read a mar345 image header """ 
 49          # clip was not used anywhere - commented out 
 50          # clip = '\x00' 
 51          #using a couple of local variables inside this function 
 52          f = infile 
 53          h = {} 
 54   
 55          #header is 4096 bytes long 
 56          l = f.read(64) 
 57          #the contents of the mar345 header is taken to be as 
 58          # described in 
 59          # http://www.mar-usa.com/support/downloads/mar345_formats.pdf 
 60          #the first 64 bytes are 4-byte integers (but in the CBFlib 
 61          # example image it seems to 128 bytes?) 
 62          #first 4-byte integer is a marker to check endianness 
 63          # TODO: turn this into a real check 
 64          if (l[0:4] == '1234'): 
 65              fs = 'I' 
 66          # unsigned integer, was using unsigned long (64 bit?) 
 67          fs = 'i' 
 68          #image dimensions 
 69          self.dim1 = self.dim2 = int(struct.unpack(fs, l[4:8])[0]) 
 70          #number of high intensity pixels 
 71          self.numhigh = struct.unpack(fs, l[2 * 4 : (2 + 1) * 4])[0] 
 72          h['NumHigh'] = self.numhigh 
 73          #Image format 
 74          i = struct.unpack(fs, l[3 * 4 : (3 + 1) * 4])[0] 
 75          if i == 1: 
 76              h['Format'] = 'compressed' 
 77          elif i == 2: 
 78              h['Format'] = 'spiral' 
 79          else: 
 80              h['Format'] = 'compressed' 
 81              print "warning: image format could not be detetermined" + \ 
 82                  "- assuming compressed mar345" 
 83          #collection mode 
 84          h['Mode'] = {0:'Dose', 1: 'Time'}[struct.unpack(fs, l[4 * 4:(4 + 1) * 4])[0]] 
 85          #total number of pixels 
 86          self.numpixels = struct.unpack(fs, l[5 * 4:(5 + 1) * 4])[0] 
 87          h['NumPixels'] = str(self.numpixels) 
 88          #pixel dimensions (length,height) in mm 
 89          h['PixelLength'] = struct.unpack(fs, l[6 * 4:(6 + 1) * 4])[0] / 1000.0 
 90          h['PixelHeight'] = struct.unpack(fs, l[7 * 4:(7 + 1) * 4])[0] / 1000.0 
 91          #x-ray wavelength in AA 
 92          h['Wavelength'] = struct.unpack(fs, l[8 * 4:(8 + 1) * 4])[0] / 1000000.0 
 93          #used distance 
 94          h['Distance'] = struct.unpack(fs, l[9 * 4:(9 + 1) * 4])[0] / 1000.0 
 95          #starting and ending phi 
 96          h['StartPhi'] = struct.unpack(fs, l[10 * 4:11 * 4])[0] / 1000.0 
 97          h['EndPhi'] = struct.unpack(fs, l[11 * 4:12 * 4])[0] / 1000.0 
 98          #starting and ending omega 
 99          h['StartOmega'] = struct.unpack(fs, l[12 * 4:13 * 4])[0] / 1000.0 
100          h['EndOmega'] = struct.unpack(fs, l[13 * 4:14 * 4])[0] / 1000.0 
101          #Chi and Twotheta angles 
102          h['Chi'] = struct.unpack(fs, l[14 * 4:15 * 4])[0] / 1000.0 
103          h['TwoTheta'] = struct.unpack(fs, l[15 * 4:16 * 4])[0] / 1000.0 
104   
105          #the rest of the header is ascii 
106          # TODO: validate these values against the binaries already read 
107          l = f.read(128) 
108          if not 'mar research' in l: 
109              print "warning: the string \"mar research\" should be in " + \ 
110                  "bytes 65-76 of the header but was not" 
111          l = string.strip(f.read(4096 - 128 - 64)) 
112          for m in l.splitlines(): 
113              if m == 'END OF HEADER': break 
114              n = m.split(' ', 1) 
115              if n[0] == '': 
116                  continue 
117              if n[0] in ('PROGRAM', 'DATE', 'SCANNER', 'HIGH', 'MULTIPLIER', 
118                          'GAIN', 'WAVELENGTH', 'DISTANCE', 'RESOLUTION', 
119                          'CHI', 'TWOTHETA', 'MODE', 'TIME', 'GENERATOR', 
120                          'MONOCHROMATOR', 'REMARK'): 
121                  h[n[0]] = n[1].strip() 
122                  continue 
123              if n[0] in ('FORMAT'): 
124                  (h['DIM'], h['FORMAT_TYPE'], h['NO_PIXELS']) = n[1].split() 
125                  continue 
126              if n[0] in ('PIXEL', 'OFFSET', 'PHI', 'OMEGA', 'COUNTS', 
127                          'CENTER', 'INTENSITY', 'HISTOGRAM', 'COLLIMATOR'): 
128                  n = m.split() 
129                  h.update([(n[0] + '_' + n[j], n[j + 1]) for j in range(1, len(n), 2)]) 
130                  continue 
131          self.header = h 
132          return h 
133   
134 -    def write(self): 
135          pass 
136