Mercurial > pylearn

annotate amat.py @ 474:40c8a46b3da7

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
added Stopper.find_min
author James Bergstra <bergstrj@iro.umontreal.ca>
date Thu, 23 Oct 2008 18:05:46 -0400
parents bd937e845bbb
children
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 class AMat:
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
6 """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
7
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
8 Attributes:
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
9
470
bd937e845bbb new stuff: algorithms/logistic_regression, datasets/MNIST
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 266
diff changeset
10 input -- all columns of input
bd937e845bbb new stuff: algorithms/logistic_regression, datasets/MNIST
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 266
diff changeset
11 target -- all columns of target
bd937e845bbb new stuff: algorithms/logistic_regression, datasets/MNIST
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 266
diff changeset
12 weight -- all columns of weight
bd937e845bbb new stuff: algorithms/logistic_regression, datasets/MNIST
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 266
diff changeset
13 extra -- all columns of extra
266
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
14
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
15 all -- the entire data contents of the amat file
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
16 n_examples -- the number of training examples in the file
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 AMat stands for Ascii Matri[x,ces]
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
19
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
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
22 marker_size = '#size:'
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
23 marker_sizes = '#sizes:'
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
24 marker_col_names = '#:'
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
25
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
26 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
27
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
28 """Load the amat at <path> into memory.
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
29
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
30 path - str: location of amat file
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
31 head - int: stop reading after this many data rows
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
32 update_interval - int: print '.' to ofile every <this many> lines
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
33 ofile - file: print status, msgs, etc. to this file
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
34
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
35 """
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
36 self.all = None
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
37 self.input = None
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
38 self.target = None
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
39 self.weight = None
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
40 self.extra = None
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
41
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
42 self.header = False
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
43 self.header_size = None
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
44 self.header_rows = None
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
45 self.header_cols = None
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
46 self.header_sizes = None
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
47 self.header_col_names = []
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
48
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
49 data_started = False
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
50 data = array.array('d')
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 f = open(path)
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
53 n_data_lines = 0
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
54 len_float_line = None
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
55
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
56 for i,line in enumerate(f):
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
57 if n_data_lines == head:
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
58 #we've read enough data,
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
59 # break even if there's more in the file
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
60 break
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
61 if len(line) == 0 or line == '\n':
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
62 continue
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
63 if line[0] == '#':
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
64 if not data_started:
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
65 #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
66 # some header line
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
67 self.header = True
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
68 if line.startswith(AMat.marker_size):
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
69 info = line[len(AMat.marker_size):]
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
70 self.header_size = [int(s) for s in info.split()]
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
71 self.header_rows, self.header_cols = self.header_size
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
72 if line.startswith(AMat.marker_col_names):
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
73 info = line[len(AMat.marker_col_names):]
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
74 self.header_col_names = info.split()
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
75 elif line.startswith(AMat.marker_sizes):
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
76 info = line[len(AMat.marker_sizes):]
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
77 self.header_sizes = [int(s) for s in info.split()]
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
78 else:
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
79 #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
80 data_started = True
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
81 float_line = [float(s) for s in line.split()]
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
82 if len_float_line is None:
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
83 len_float_line = len(float_line)
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
84 if (self.header_cols is not None) \
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
85 and self.header_cols != len_float_line:
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
86 print >> sys.stderr, \
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
87 '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
88 self.header_cols, len_float_line, len_float_line
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
89 else:
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
90 if len_float_line != len(float_line):
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
91 raise IOError('wrong line length', i, line)
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
92 data.extend(float_line)
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
93 n_data_lines += 1
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
94
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
95 if update_interval > 0 and (ofile is not None) \
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
96 and n_data_lines % update_interval == 0:
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
97 ofile.write('.')
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
98 ofile.flush()
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
99
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
100 if update_interval > 0:
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
101 ofile.write('\n')
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
102 f.close()
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
103
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
104 # convert from array.array to numpy.ndarray
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
105 nshape = (len(data) / len_float_line, len_float_line)
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
106 self.all = numpy.frombuffer(data).reshape(nshape)
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
107 self.n_examples = self.all.shape[0]
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
108
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
109 # assign
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
110 if self.header_sizes is not None:
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
111 if len(self.header_sizes) > 4:
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
112 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
113 leftmost = 0
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
114 #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
115 # the loop will exit before 4 iterations
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
116 attrlist = ['input', 'target', 'weight', 'extra']
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
117 for attr, ncols in zip(attrlist, self.header_sizes):
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
118 setattr(self, attr, self.all[:, leftmost:leftmost+ncols])
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
119 leftmost += ncols
6e69fb91f3c0 initial commit of amat
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
diff changeset
120