Source Code for Module Volume.IO.dxReader

 1  import Numeric 
 2  from string import split 
 3  from  Volume.Grid3D import Grid3DF, Grid3DSI, Grid3DUC 
 4   
 5 -class ReadDX: 
 6   
 7 -    def __init__(self): 
 8          self.header = {} 
 9          self.filename = None 
10   
11   
12 -    def read(self, filename, normalize): 
13          self.filename = filename 
14          data = self.readAllLines(filename) 
15          return self.parse(data, normalize) 
16       
17   
18 -    def readAllLines(self, filename): 
19          # open file to read 
20          f = open(filename, 'r') 
21          data = f.readlines() 
22          f.close() 
23          return data 
24   
25           
26 -    def parse(self, data, normalize): 
27   
28          h = self.header = {} 
29      
30          # read header (need some specs here) 
31          w = split(data[4]) 
32          nx, ny, nz = int(w[5]), int(w[6]), int(w[7]) 
33          h['nx']=nx; h['ny']=ny; h['nz']=nz 
34   
35          w = split(data[5]) 
36          ox, oy, oz = float(w[1]), float(w[2]), float(w[3]) 
37          h['origin']= (ox, oy, oz) 
38   
39          w = split(data[6]) 
40          h['stepx'] = sx = float(w[1]) 
41   
42          w = split(data[7]) 
43          h['stepy'] = sy = float(w[2]) 
44   
45          w = split(data[8]) 
46          h['stepz'] = sz = float(w[3]) 
47   
48          self.data = array = Numeric.zeros( (nx,ny,nz), Numeric.Float32) 
49          values = map(split, data[11:-5]) 
50          ind=0 
51          size = nx*ny*nz 
52          for line in values: 
53              if ind>=size: 
54                  break 
55              l = len(line) 
56              array.flat[ind:ind+l] = map(float, line) 
57              ind = ind + l 
58   
59          stepSize = [h['stepx'], h['stepy'], h['stepz']] 
60          volume = Grid3DF(self.data, h['origin'], stepSize, h) 
61          return volume 
62   
63   
64 -    def describe(self): 
65          print "DX file: ", self.filename 
66          print "nx= ", self.header['nx'] 
67          print "ny= ", self.header['ny']  
68          print "nz= ", self.header['nz']  
69          #print "xlen= ", self.header['xlen']  
70          #print "ylen= ", self.header['ylen']  
71          #print "zlen= ", self.header['zlen'] 
72          print "min= ", min(self.data.flat) 
73          print "max= ", max(self.data.flat) 
74          #print "mean= ", self.header['amean'] 
75          print "origin= ", self.header['origin']  
76   
77   
78  if __name__=='__main__': 
79      reader = ReadDX() 
80      header, vol = reader.read("pot-0mM.dx") 
81      reader.describe() 
82