Source Code for Module fabio.fit2dmaskimage

 1  ## Automatically adapted for numpy.oldnumeric Oct 05, 2007 by alter_code1.py 
 2   
 3  #!/usr/bin/env python 
 4  """ 
 5   
 6  Author: Andy Hammersley, ESRF 
 7  Translation into python/fabio: Jon Wright, ESRF 
 8  """ 
 9   
10  import numpy 
11   
12  from fabioimage import fabioimage 
13   
14   
15 -class fit2dmaskimage(fabioimage): 
16      """ Read and try to write Andy Hammersley's mask format """ 
17   
18   
19 -    def _readheader(self, infile): 
20          """ 
21          Read in a header from an already open file 
22          """ 
23          # 1024 bytes gives 256x32 bit integers 
24          header = infile.read(1024) 
25          for i, j in [ ("M", 0), 
26                        ("A", 4), 
27                        ("S", 8), 
28                        ("K", 12)  ]: 
29              if header[j] != i: 
30                  raise Exception("Not a fit2d mask file") 
31          fit2dhdr = numpy.fromstring(header, numpy.int32) 
32          self.dim1 = fit2dhdr[4] # 1 less than Andy's fortran 
33          self.dim2 = fit2dhdr[5] 
34   
35   
36 -    def read(self, fname): 
37          """ 
38          Read in header into self.header and 
39              the data   into self.data 
40          """ 
41          fin = self._open(fname) 
42          self._readheader(fin) 
43          # Compute image size 
44          self.bytecode = numpy.uint8 
45          self.bpp = len(numpy.array(0, self.bytecode).tostring()) 
46   
47          # integer division 
48          num_ints = (self.dim1 + 31) // 32 
49          total = self.dim2 * num_ints * 4 
50          data = fin.read(total) 
51          assert len(data) == total 
52          fin.close() 
53   
54          # Now to unpack it 
55          data = numpy.fromstring(data, numpy.uint8) 
56          data = numpy.reshape(data, (self.dim2, num_ints * 4)) 
57   
58          result = numpy.zeros((self.dim2, num_ints * 4 * 8), numpy.uint8) 
59   
60          # Unpack using bitwise comparisons to 2**n 
61          bits = numpy.ones((1), numpy.uint8) 
62          for i in range(8): 
63              temp = numpy.bitwise_and(bits, data) 
64              result[:, i::8] = temp.astype(numpy.uint8) 
65              bits = bits * 2 
66          # Extra rows needed for packing odd dimensions 
67          spares = num_ints * 4 * 8 - self.dim1 
68          if spares == 0: 
69              self.data = numpy.where(result == 0, 0, 1) 
70          else: 
71              self.data = numpy.where(result[:, :-spares] == 0, 0, 1) 
72          # Transpose appears to be needed to match edf reader (scary??) 
73  #        self.data = numpy.transpose(self.data) 
74          self.data = numpy.reshape(self.data.astype(numpy.uint16), 
75                                      (self.dim2, self.dim1)) 
76          self.pilimage = None 
77   
78   
79   
80 -    def write(self, fname): 
81          """ 
82          Try to write a file 
83          check we can write zipped also 
84          mimics that fabian was writing uint16 (we sometimes want floats) 
85          """ 
86          raise Exception("Not implemented yet") 
87