Source Code for Module Volume.IO.gamessOrbitalsReader

 1  import Numeric 
 2  from string import split 
 3   
 4 -class ReadGamessOrbitals: 
 5      """Read a rawiv binary file""" 
 6       
 7 -    def mapArray(self, values, mini, maxi): 
 8   
 9          # allocate numeric array that is **2 
10          dim = int(round(len(values)**(1./3))) 
11          print dim, dim**3, len(values) 
12          if dim**3!=len(values): 
13              raise ValueError, "Length of array is not **3" 
14          dim2 = 2 
15          while dim2<dim: 
16              dim2 = dim2*2 
17          print 'dim: padding from:', dim, 'to:', dim2 
18          intval = Numeric.zeros( (dim2,dim2,dim2), Numeric.UnsignedInt8 ) 
19   
20          valuesN = Numeric.array(values) 
21           
22          minim = min(values) 
23          maxim = max(values) 
24          scale = (maxi - mini)/float(maxim - minim) 
25          valuesN.shape = (dim, dim, dim) 
26   
27          for i in range(dim): 
28              face = valuesN[i] 
29              for j in range(dim): 
30                  line = face[j] 
31                  for k in range(dim): 
32                      intval[i][j][k] = ((line[k]-minim)*scale) + mini 
33          return intval, minim, maxim 
34   
35   
36 -    def read(self, filename): 
37           
38          myfile = open(filename) 
39          data = myfile.readlines() 
40          myfile.close() 
41          self.header = {} 
42   
43          dataspl = map( split, data ) 
44          values = [] 
45          for l in dataspl: 
46              values.extend( map(float, l) ) 
47   
48          # Fixme this should be done in separate nodes 
49          self.data, mini, maxi = self.mapArray(values, 1, 255) 
50          w, h, d = self.data.shape 
51          self.header['width'] = w 
52          self.header['height'] = h 
53          self.header['depth'] = d 
54          self.header['minif'] = mini 
55          self.header['maxif'] = maxi 
56   
57          return self.header, self.data 
58