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annotate pmat.py @ 114:d6d42a0c1275

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file copied from PLearn/python_modules/plearn/vmat/PMat.py
author Frederic Bastien <bastienf@iro.umontreal.ca>
date Wed, 07 May 2008 12:18:11 -0400
parents
children 01aa97a2212d
rev   line source
114
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
1 ## Automatically adapted for numpy.numarray Jun 13, 2007 by python_numarray_to_numpy (-xsm)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
2
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
3 # PMat.py
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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4 # Copyright (C) 2005 Pascal Vincent
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
5 #
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
6 # Redistribution and use in source and binary forms, with or without
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
7 # modification, are permitted provided that the following conditions are met:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
8 #
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
9 # 1. Redistributions of source code must retain the above copyright
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
10 # notice, this list of conditions and the following disclaimer.
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
11 #
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
12 # 2. Redistributions in binary form must reproduce the above copyright
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
13 # notice, this list of conditions and the following disclaimer in the
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
14 # documentation and/or other materials provided with the distribution.
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
15 #
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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16 # 3. The name of the authors may not be used to endorse or promote
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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17 # products derived from this software without specific prior written
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
18 # permission.
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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19 #
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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20 # THIS SOFTWARE IS PROVIDED BY THE AUTHORS ``AS IS'' AND ANY EXPRESS OR
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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21 # IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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22 # OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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23 # NO EVENT SHALL THE AUTHORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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24 # SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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25 # TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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26 # PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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27 # LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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28 # NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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29 # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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30 #
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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31 # This file is part of the PLearn library. For more information on the PLearn
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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32 # library, go to the PLearn Web site at www.plearn.org
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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33
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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34
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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35 # Author: Pascal Vincent
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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36
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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37 #import numarray, sys, os, os.path
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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38 import numpy.numarray, sys, os, os.path
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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39 pyplearn_import_failed = False
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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40 try:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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41 from plearn.pyplearn.plearn_repr import plearn_repr, format_list_elements
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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42 except ImportError:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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43 pyplearn_import_failed = True
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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44
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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45
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
46
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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47 def array_columns( a, cols ):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
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48 indices = None
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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49 if isinstance( cols, int ):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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50 indices = [ cols ]
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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51 elif isinstance( cols, slice ):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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52 #print cols
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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53 indices = range( *cols.indices(cols.stop) )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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54 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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55 indices = list( cols )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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56
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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57 return numpy.numarray.take(a, indices, axis=1)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
58
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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59 def load_pmat_as_array(fname):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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60 s = file(fname,'rb').read()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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61 formatstr = s[0:64]
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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62 datastr = s[64:]
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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63 structuretype, l, w, data_type, endianness = formatstr.split()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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64
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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65 if data_type=='DOUBLE':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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66 elemtype = 'd'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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67 elif data_type=='FLOAT':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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68 elemtype = 'f'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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69 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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70 raise ValueError('Invalid data type in file header: '+data_type)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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71
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
72 if endianness=='LITTLE_ENDIAN':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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73 byteorder = 'little'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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74 elif endianness=='BIG_ENDIAN':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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75 byteorder = 'big'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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76 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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77 raise ValueError('Invalid endianness in file header: '+endianness)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
78
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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79 l = int(l)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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80 w = int(w)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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81 X = numpy.numarray.fromstring(datastr,elemtype, shape=(l,w) )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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82 if byteorder!=sys.byteorder:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
83 X.byteswap(True)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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84 return X
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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85
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
86 def save_array_as_pmat( fname, ar, fieldnames=[] ):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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87 s = file(fname,'wb')
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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88
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
89 length, width = ar.shape
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
90 if fieldnames:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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91 assert len(fieldnames) == width
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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92 metadatadir = fname+'.metadata'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
93 if not os.path.isdir(metadatadir):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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94 os.mkdir(metadatadir)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
95 fieldnamefile = os.path.join(metadatadir,'fieldnames')
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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96 f = open(fieldnamefile,'wb')
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
97 for name in fieldnames:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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98 f.write(name+'\t0\n')
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
99 f.close()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
100
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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101 header = 'MATRIX ' + str(length) + ' ' + str(width) + ' '
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
102 if ar.dtype.char=='d':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
103 header += 'DOUBLE '
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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104 elemsize = 8
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
105
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
106 elif ar.dtype.char=='f':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
107 header += 'FLOAT '
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
108 elemsize = 4
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
109
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
110 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
111 raise TypeError('Unsupported typecode: %s' % ar.dtype.char)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
112
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
113 rowsize = elemsize*width
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
114
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
115 if sys.byteorder=='little':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
116 header += 'LITTLE_ENDIAN '
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
117 elif sys.byteorder=='big':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
118 header += 'BIG_ENDIAN '
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
119 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
120 raise TypeError('Unsupported sys.byteorder: '+repr(sys.byteorder))
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
121
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
122 header += ' '*(63-len(header))+'\n'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
123 s.write( header )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
124 s.write( ar.tostring() )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
125 s.close()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
126
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
127
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
128 ####### Iterators ###########################################################
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
129
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
130 class VMatIt:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
131 def __init__(self, vmat):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
132 self.vmat = vmat
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
133 self.cur_row = 0
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
134
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
135 def __iter__(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
136 return self
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
137
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
138 def next(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
139 if self.cur_row==self.vmat.length:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
140 raise StopIteration
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
141 row = self.vmat.getRow(self.cur_row)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
142 self.cur_row += 1
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
143 return row
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
144
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
145 class ColumnIt:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
146 def __init__(self, vmat, col):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
147 self.vmat = vmat
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
148 self.col = col
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
149 self.cur_row = 0
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
150
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
151 def __iter__(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
152 return self
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
153
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
154 def next(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
155 if self.cur_row==self.vmat.length:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
156 raise StopIteration
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
157 val = self.vmat[self.cur_row, self.col]
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
158 self.cur_row += 1
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
159 return val
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
160
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
161 ####### VMat classes ########################################################
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
162
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
163 class VMat:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
164 def __iter__(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
165 return VMatIt(self)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
166
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
167 def __getitem__( self, key ):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
168 if isinstance( key, slice ):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
169 start, stop, step = key.start, key.stop, key.step
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
170 if step!=None:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
171 raise IndexError('Extended slice with step not currently supported')
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
172
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
173 if start is None:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
174 start = 0
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
175
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
176 l = self.length
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
177 if stop is None or stop > l:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
178 stop = l
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
179
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
180 return self.getRows(start,stop-start)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
181
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
182 elif isinstance( key, tuple ):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
183 # Basically returns a SubVMatrix
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
184 assert len(key) == 2
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
185 rows = self.__getitem__( key[0] )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
186
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
187 shape = rows.shape
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
188 if len(shape) == 1:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
189 return rows[ key[1] ]
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
190
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
191 cols = key[1]
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
192 if isinstance(cols, slice):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
193 start, stop, step = cols.start, cols.stop, cols.step
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
194 if start is None:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
195 start = 0
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
196
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
197 if stop is None:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
198 stop = self.width
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
199 elif stop < 0:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
200 stop = self.width+stop
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
201
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
202 cols = slice(start, stop, step)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
203
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
204 return array_columns(rows, cols)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
205
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
206 elif isinstance( key, str ):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
207 # The key is considered to be a fieldname and a column is
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
208 # returned.
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
209 try:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
210 return array_columns( self.getRows(0,self.length),
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
211 self.fieldnames.index(key) )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
212 except ValueError:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
213 print >>sys.stderr, "Key is '%s' while fieldnames are:" % key
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
214 print >>sys.stderr, self.fieldnames
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
215 raise
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
216
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
217 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
218 if key<0: key+=self.length
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
219 return self.getRow(key)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
220
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
221 def getFieldIndex(self, fieldname):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
222 try:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
223 return self.fieldnames.index(fieldname)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
224 except ValueError:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
225 raise ValueError( "VMat has no field named %s. Field names: %s"
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
226 %(fieldname, ','.join(self.fieldnames)) )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
227
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
228 class PMat( VMat ):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
229
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
230 def __init__(self, fname, openmode='r', fieldnames=[], elemtype='d',
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
231 inputsize=-1, targetsize=-1, weightsize=-1, array = None):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
232 self.fname = fname
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
233 self.inputsize = inputsize
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
234 self.targetsize = targetsize
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
235 self.weightsize = weightsize
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
236 if openmode=='r':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
237 self.f = open(fname,'rb')
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
238 self.read_and_parse_header()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
239 self.load_fieldnames()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
240
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
241 elif openmode=='w':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
242 self.f = open(fname,'w+b')
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
243 self.fieldnames = fieldnames
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
244 self.save_fieldnames()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
245 self.length = 0
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
246 self.width = len(fieldnames)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
247 self.elemtype = elemtype
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
248 self.swap_bytes = False
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
249 self.write_header()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
250
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
251 elif openmode=='a':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
252 self.f = open(fname,'r+b')
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
253 self.read_and_parse_header()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
254 self.load_fieldnames()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
255
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
256 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
257 raise ValueError("Currently only supported openmodes are 'r', 'w' and 'a': "+repr(openmode)+" is not supported")
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
258
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
259 if array is not None:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
260 shape = array.shape
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
261 if len(shape) == 1:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
262 row_format = lambda r: [ r ]
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
263 elif len(shape) == 2:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
264 row_format = lambda r: r
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
265
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
266 for row in array:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
267 self.appendRow( row_format(row) )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
268
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
269 def __del__(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
270 self.close()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
271
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
272 def write_header(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
273 header = 'MATRIX ' + str(self.length) + ' ' + str(self.width) + ' '
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
274
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
275 if self.elemtype=='d':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
276 header += 'DOUBLE '
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
277 self.elemsize = 8
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
278 elif self.elemtype=='f':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
279 header += 'FLOAT '
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
280 self.elemsize = 4
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
281 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
282 raise TypeError('Unsupported elemtype: '+repr(elemtype))
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
283 self.rowsize = self.elemsize*self.width
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
284
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
285 if sys.byteorder=='little':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
286 header += 'LITTLE_ENDIAN '
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
287 elif sys.byteorder=='big':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
288 header += 'BIG_ENDIAN '
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
289 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
290 raise TypeError('Unsupported sys.byteorder: '+repr(sys.byteorder))
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
291
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
292 header += ' '*(63-len(header))+'\n'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
293
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
294 self.f.seek(0)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
295 self.f.write(header)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
296
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
297 def read_and_parse_header(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
298 header = self.f.read(64)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
299 mat_type, l, w, data_type, endianness = header.split()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
300 if mat_type!='MATRIX':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
301 raise ValueError('Invalid file header (should start with MATRIX)')
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
302 self.length = int(l)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
303 self.width = int(w)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
304 if endianness=='LITTLE_ENDIAN':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
305 byteorder = 'little'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
306 elif endianness=='BIG_ENDIAN':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
307 byteorder = 'big'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
308 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
309 raise ValueError('Invalid endianness in file header: '+endianness)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
310 self.swap_bytes = (byteorder!=sys.byteorder)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
311
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
312 if data_type=='DOUBLE':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
313 self.elemtype = 'd'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
314 self.elemsize = 8
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
315 elif data_type=='FLOAT':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
316 self.elemtype = 'f'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
317 self.elemsize = 4
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
318 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
319 raise ValueError('Invalid data type in file header: '+data_type)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
320 self.rowsize = self.elemsize*self.width
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
321
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
322 def load_fieldnames(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
323 self.fieldnames = []
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
324 fieldnamefile = os.path.join(self.fname+'.metadata','fieldnames')
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
325 if os.path.isfile(fieldnamefile):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
326 f = open(fieldnamefile)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
327 for row in f:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
328 row = row.split()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
329 if len(row)>0:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
330 self.fieldnames.append(row[0])
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
331 f.close()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
332 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
333 self.fieldnames = [ "field_"+str(i) for i in range(self.width) ]
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
334
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
335 def save_fieldnames(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
336 metadatadir = self.fname+'.metadata'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
337 if not os.path.isdir(metadatadir):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
338 os.mkdir(metadatadir)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
339 fieldnamefile = os.path.join(metadatadir,'fieldnames')
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
340 f = open(fieldnamefile,'wb')
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
341 for name in self.fieldnames:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
342 f.write(name+'\t0\n')
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
343 f.close()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
344
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
345 def getRow(self,i):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
346 if i<0 or i>=self.length:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
347 raise IndexError('PMat index out of range')
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
348 self.f.seek(64+i*self.rowsize)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
349 data = self.f.read(self.rowsize)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
350 ar = numpy.numarray.fromstring(data, self.elemtype, (self.width,))
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
351 if self.swap_bytes:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
352 ar.byteswap(True)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
353 return ar
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
354
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
355 def getRows(self,i,l):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
356 if i<0 or l<0 or i+l>self.length:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
357 raise IndexError('PMat index out of range')
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
358 self.f.seek(64+i*self.rowsize)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
359 data = self.f.read(l*self.rowsize)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
360 ar = numpy.numarray.fromstring(data, self.elemtype, (l,self.width))
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
361 if self.swap_bytes:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
362 ar.byteswap(True)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
363 return ar
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
364
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
365 def checkzerorow(self,i):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
366 if i<0 or i>self.length:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
367 raise IndexError('PMat index out of range')
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
368 self.f.seek(64+i*self.rowsize)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
369 data = self.f.read(self.rowsize)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
370 ar = numpy.numarray.fromstring(data, self.elemtype, (len(data)/self.elemsize,))
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
371 if self.swap_bytes:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
372 ar.byteswap(True)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
373 for elem in ar:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
374 if elem!=0:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
375 return False
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
376 return True
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
377
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
378 def putRow(self,i,row):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
379 if i<0 or i>=self.length:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
380 raise IndexError('PMat index out of range')
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
381 if len(row)!=self.width:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
382 raise TypeError('length of row ('+str(len(row))+ ') differs from matrix width ('+str(self.width)+')')
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
383 if i<0 or i>=self.length:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
384 raise IndexError
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
385 if self.swap_bytes: # must make a copy and swap bytes
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
386 ar = numpy.numarray.numarray(row,type=self.elemtype)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
387 ar.byteswap(True)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
388 else: # asarray makes a copy if not already a numarray of the right type
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
389 ar = numpy.numarray.asarray(row,type=self.elemtype)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
390 self.f.seek(64+i*self.rowsize)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
391 self.f.write(ar.tostring())
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
392
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
393 def appendRow(self,row):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
394 if len(row)!=self.width:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
395 raise TypeError('length of row ('+str(len(row))+ ') differs from matrix width ('+str(self.width)+')')
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
396 if self.swap_bytes: # must make a copy and swap bytes
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
397 ar = numpy.numarray.numarray(row,type=self.elemtype)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
398 ar.byteswap(True)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
399 else: # asarray makes a copy if not already a numarray of the right type
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
400 ar = numpy.numarray.asarray(row,type=self.elemtype)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
401
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
402 self.f.seek(64+self.length*self.rowsize)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
403 self.f.write(ar.tostring())
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
404 self.length += 1
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
405 self.write_header() # update length in header
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
406
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
407 def flush(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
408 self.f.flush()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
409
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
410 def close(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
411 if hasattr(self, 'f'):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
412 self.f.close()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
413
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
414 def append(self,row):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
415 self.appendRow(row)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
416
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
417 def __setitem__(self, i, row):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
418 l = self.length
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
419 if i<0: i+=l
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
420 self.putRow(i,row)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
421
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
422 def __len__(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
423 return self.length
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
424
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
425 if not pyplearn_import_failed:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
426 def __str__( self ):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
427 return plearn_repr(self, indent_level=0)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
428
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
429 def plearn_repr( self, indent_level=0, inner_repr=plearn_repr ):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
430 # asking for plearn_repr could be to send specification over
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
431 # to another prg so that will open the .pmat
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
432 # So we make sure data is flushed to disk.
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
433 self.flush()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
434
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
435 def elem_format( elem ):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
436 k, v = elem
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
437 return '%s = %s' % ( k, inner_repr(v, indent_level+1) )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
438
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
439 options = [ ( 'filename', self.fname ),
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
440 ( 'inputsize', self.inputsize ),
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
441 ( 'targetsize', self.targetsize ),
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
442 ( 'weightsize', self.weightsize ) ]
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
443 return 'FileVMatrix(%s)' % format_list_elements( options, elem_format, indent_level+1 )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
444
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
445 if __name__ == '__main__':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
446 pmat = PMat( 'tmp.pmat', 'w', fieldnames=['F1', 'F2'] )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
447 pmat.append( [1, 2] )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
448 pmat.append( [3, 4] )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
449 pmat.close()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
450
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
451 pmat = PMat( 'tmp.pmat', 'r' )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
452 print pmat
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
453 print pmat[:]
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
454 # print "+++ tmp.pmat contains: "
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
455 # os.system( 'plearn vmat cat tmp.pmat' )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
456
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
457 os.remove( 'tmp.pmat' )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
458 if os.path.exists( 'tmp.pmat.metadata' ):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
459 import shutil
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
diff changeset
460 shutil.rmtree( 'tmp.pmat.metadata' )