annotate amat.py @ 432:8e4d2ebd816a

added a test for LinearRegression
author Yoshua Bengio <bengioy@iro.umontreal.ca>
date Tue, 29 Jul 2008 11:16:05 -0400
parents 6e69fb91f3c0
children bd937e845bbb
rev   line source
266
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
1 """load PLearn AMat files"""
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
2
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
3 import sys, numpy, array
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
4
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
5 path_MNIST = '/u/bergstrj/pub/data/mnist.amat'
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
6
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
7
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
8 class AMat:
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
9 """DataSource to access a plearn amat file as a periodic unrandomized stream.
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
10
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
11 Attributes:
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
12
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
13 input -- minibatch of input
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
14 target -- minibatch of target
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
15 weight -- minibatch of weight
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
16 extra -- minitbatch of extra
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
17
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
18 all -- the entire data contents of the amat file
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
19 n_examples -- the number of training examples in the file
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
20
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
21 AMat stands for Ascii Matri[x,ces]
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
22
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
23 """
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
24
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
25 marker_size = '#size:'
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
26 marker_sizes = '#sizes:'
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
27 marker_col_names = '#:'
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
28
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
29 def __init__(self, path, head=None, update_interval=0, ofile=sys.stdout):
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
30
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
31 """Load the amat at <path> into memory.
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
32
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
33 path - str: location of amat file
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
34 head - int: stop reading after this many data rows
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
35 update_interval - int: print '.' to ofile every <this many> lines
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
36 ofile - file: print status, msgs, etc. to this file
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
37
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
38 """
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
39 self.all = None
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
40 self.input = None
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
41 self.target = None
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
42 self.weight = None
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
43 self.extra = None
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
44
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
45 self.header = False
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
46 self.header_size = None
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
47 self.header_rows = None
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
48 self.header_cols = None
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
49 self.header_sizes = None
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
50 self.header_col_names = []
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
51
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
52 data_started = False
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
53 data = array.array('d')
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
54
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
55 f = open(path)
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
56 n_data_lines = 0
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
57 len_float_line = None
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
58
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
59 for i,line in enumerate(f):
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
60 if n_data_lines == head:
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
61 #we've read enough data,
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
62 # break even if there's more in the file
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
63 break
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
64 if len(line) == 0 or line == '\n':
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
65 continue
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
66 if line[0] == '#':
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
67 if not data_started:
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
68 #the condition means that the file has a header, and we're on
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
69 # some header line
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
70 self.header = True
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
71 if line.startswith(AMat.marker_size):
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
72 info = line[len(AMat.marker_size):]
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
73 self.header_size = [int(s) for s in info.split()]
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
74 self.header_rows, self.header_cols = self.header_size
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
75 if line.startswith(AMat.marker_col_names):
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
76 info = line[len(AMat.marker_col_names):]
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
77 self.header_col_names = info.split()
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
78 elif line.startswith(AMat.marker_sizes):
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
79 info = line[len(AMat.marker_sizes):]
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
80 self.header_sizes = [int(s) for s in info.split()]
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
81 else:
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
82 #the first non-commented line tells us that the header is done
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
83 data_started = True
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
84 float_line = [float(s) for s in line.split()]
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
85 if len_float_line is None:
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
86 len_float_line = len(float_line)
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
87 if (self.header_cols is not None) \
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
88 and self.header_cols != len_float_line:
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
89 print >> sys.stderr, \
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
90 'WARNING: header declared %i cols but first line has %i, using %i',\
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
91 self.header_cols, len_float_line, len_float_line
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
92 else:
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
93 if len_float_line != len(float_line):
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
94 raise IOError('wrong line length', i, line)
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
95 data.extend(float_line)
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
96 n_data_lines += 1
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
97
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
98 if update_interval > 0 and (ofile is not None) \
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
99 and n_data_lines % update_interval == 0:
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
100 ofile.write('.')
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
101 ofile.flush()
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
102
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
103 if update_interval > 0:
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
104 ofile.write('\n')
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
105 f.close()
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
106
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
107 # convert from array.array to numpy.ndarray
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
108 nshape = (len(data) / len_float_line, len_float_line)
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
109 self.all = numpy.frombuffer(data).reshape(nshape)
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
110 self.n_examples = self.all.shape[0]
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
111
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
112 # assign
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
113 if self.header_sizes is not None:
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
114 if len(self.header_sizes) > 4:
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
115 print >> sys.stderr, 'WARNING: ignoring sizes after 4th in %s' % path
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
116 leftmost = 0
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
117 #here we make use of the fact that if header_sizes has len < 4
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
118 # the loop will exit before 4 iterations
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
119 attrlist = ['input', 'target', 'weight', 'extra']
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
120 for attr, ncols in zip(attrlist, self.header_sizes):
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
121 setattr(self, attr, self.all[:, leftmost:leftmost+ncols])
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
122 leftmost += ncols
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
123