pylearn: pmat.py annotate

annotate pmat.py @ 421:e01f17be270a

Kernel regression learning algorithm

author	Yoshua Bengio <bengioy@iro.umontreal.ca>
date	Sat, 19 Jul 2008 10:11:22 -0400
parents	c2f17f231960
children

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: diff changeset	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: diff changeset	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: diff changeset	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: diff changeset	19 #
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	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: diff changeset	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: diff changeset	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: diff changeset	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: diff changeset	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: diff changeset	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: diff changeset	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: diff changeset	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: diff changeset	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: diff changeset	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: diff changeset	30 #
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	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: diff changeset	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: diff changeset	33
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	34
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	35 # Author: Pascal Vincent
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	36
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	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: diff changeset	38 import numpy.numarray, sys, os, os.path
380 c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	39 import fpconst
114 d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	40
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	41 def array_columns( a, cols ):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	42 indices = None
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	43 if isinstance( cols, int ):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	44 indices = [ cols ]
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	45 elif isinstance( cols, slice ):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	46 #print cols
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	47 indices = range( *cols.indices(cols.stop) )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	48 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	49 indices = list( cols )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	50
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	51 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	52
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	53 def load_pmat_as_array(fname):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	54 s = file(fname,'rb').read()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	55 formatstr = s[0:64]
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	56 datastr = s[64:]
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	57 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: diff changeset	58
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	59 if data_type=='DOUBLE':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	60 elemtype = 'd'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	61 elif data_type=='FLOAT':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	62 elemtype = 'f'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	63 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	64 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	65
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	66 if endianness=='LITTLE_ENDIAN':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	67 byteorder = 'little'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	68 elif endianness=='BIG_ENDIAN':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	69 byteorder = 'big'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	70 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	71 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	72
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	73 l = int(l)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	74 w = int(w)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	75 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: diff changeset	76 if byteorder!=sys.byteorder:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	77 X.byteswap(True)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	78 return X
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	79
116 9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	80 def load_pmat_as_array_dataset(fname):
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	81 import dataset,lookup_list
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	82
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	83 #load the pmat as array
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	84 a=load_pmat_as_array(fname)
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	85
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	86 #load the fieldnames
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	87 fieldnames = []
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	88 fieldnamefile = os.path.join(fname+'.metadata','fieldnames')
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	89 if os.path.isfile(fieldnamefile):
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	90 f = open(fieldnamefile)
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	91 for row in f:
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	92 row = row.split()
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	93 if len(row)>0:
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	94 fieldnames.append(row[0])
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	95 f.close()
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	96 else:
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	97 self.fieldnames = [ "field_"+str(i) for i in range(a.shape[1]) ]
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	98
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	99 return dataset.ArrayDataSet(a,lookup_list.LookupList(fieldnames,[x for x in range(a.shape[1])]))
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	100
380 c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	101 def load_amat_as_array_dataset(fname):
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	102 import dataset,lookup_list
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	103
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	104 #load the amat as array
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	105 (a,fieldnames)=readAMat(fname)
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	106
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	107 #load the fieldnames
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	108 if len(fieldnames)==0:
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	109 self.fieldnames = [ "field_"+str(i) for i in range(a.shape[1]) ]
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	110
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	111 return dataset.ArrayDataSet(a,lookup_list.LookupList(fieldnames,[x for x in range(a.shape[1])]))
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	112
116 9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	113 def save_array_dataset_as_pmat(fname,ds):
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	114 ar=ds.data
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	115 save_array_as_pmat(fname,ar,ds.fieldNames())
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	116
114 d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	117 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: diff changeset	118 s = file(fname,'wb')
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	119
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	120 length, width = ar.shape
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	121 if fieldnames:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	122 assert len(fieldnames) == width
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	123 metadatadir = fname+'.metadata'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	124 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	125 os.mkdir(metadatadir)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	126 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	127 f = open(fieldnamefile,'wb')
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	128 for name in fieldnames:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	129 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	130 f.close()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	131
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	132 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	133 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	134 header += 'DOUBLE '
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	135 elemsize = 8
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	136
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	137 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	138 header += 'FLOAT '
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	139 elemsize = 4
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	140
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	141 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	142 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	143
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	144 rowsize = elemsize*width
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	145
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	146 if sys.byteorder=='little':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	147 header += 'LITTLE_ENDIAN '
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	148 elif sys.byteorder=='big':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	149 header += 'BIG_ENDIAN '
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	150 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	151 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	152
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	153 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	154 s.write( header )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	155 s.write( ar.tostring() )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	156 s.close()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	157
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	158
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	159 ####### Iterators ###########################################################
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 class VMatIt:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	162 def __init__(self, vmat):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	163 self.vmat = vmat
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	164 self.cur_row = 0
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	165
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	166 def __iter__(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	167 return self
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	168
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	169 def next(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	170 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	171 raise StopIteration
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	172 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	173 self.cur_row += 1
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	174 return row
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 class ColumnIt:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	177 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	178 self.vmat = vmat
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	179 self.col = col
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	180 self.cur_row = 0
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 def __iter__(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	183 return self
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	184
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	185 def next(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	186 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	187 raise StopIteration
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	188 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	189 self.cur_row += 1
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	190 return val
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	191
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	192 ####### VMat classes ########################################################
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	193
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	194 class VMat:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	195 def __iter__(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	196 return VMatIt(self)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	197
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	198 def __getitem__( self, key ):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	199 if isinstance( key, slice ):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	200 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	201 if step!=None:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	202 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	203
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	204 if start is None:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	205 start = 0
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	206
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	207 l = self.length
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	208 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	209 stop = l
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	210
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	211 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	212
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	213 elif isinstance( key, tuple ):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	214 # Basically returns a SubVMatrix
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	215 assert len(key) == 2
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	216 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	217
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	218 shape = rows.shape
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	219 if len(shape) == 1:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	220 return rows[ key[1] ]
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	221
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	222 cols = key[1]
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	223 if isinstance(cols, slice):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	224 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	225 if start is None:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	226 start = 0
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 if stop is None:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	229 stop = self.width
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	230 elif stop < 0:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	231 stop = self.width+stop
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	232
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	233 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	234
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	235 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	236
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	237 elif isinstance( key, str ):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	238 # 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	239 # returned.
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	240 try:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	241 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	242 self.fieldnames.index(key) )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	243 except ValueError:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	244 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	245 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	246 raise
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	247
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	248 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	249 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	250 return self.getRow(key)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	251
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	252 def getFieldIndex(self, fieldname):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	253 try:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	254 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	255 except ValueError:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	256 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	257 %(fieldname, ','.join(self.fieldnames)) )
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 class PMat( VMat ):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	260
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	261 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	262 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	263 self.fname = fname
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	264 self.inputsize = inputsize
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	265 self.targetsize = targetsize
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	266 self.weightsize = weightsize
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	267 if openmode=='r':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	268 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	269 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	270 self.load_fieldnames()
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 elif openmode=='w':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	273 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	274 self.fieldnames = fieldnames
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	275 self.save_fieldnames()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	276 self.length = 0
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	277 self.width = len(fieldnames)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	278 self.elemtype = elemtype
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	279 self.swap_bytes = False
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	280 self.write_header()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	281
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	282 elif openmode=='a':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	283 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	284 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	285 self.load_fieldnames()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	286
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	287 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	288 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	289
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	290 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	291 shape = array.shape
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	292 if len(shape) == 1:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	293 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	294 elif len(shape) == 2:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	295 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	296
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	297 for row in array:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	298 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	299
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	300 def __del__(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	301 self.close()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	302
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	303 def write_header(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	304 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	305
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	306 if self.elemtype=='d':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	307 header += 'DOUBLE '
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	308 self.elemsize = 8
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	309 elif self.elemtype=='f':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	310 header += 'FLOAT '
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	311 self.elemsize = 4
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	312 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	313 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	314 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	315
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	316 if sys.byteorder=='little':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	317 header += 'LITTLE_ENDIAN '
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	318 elif sys.byteorder=='big':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	319 header += 'BIG_ENDIAN '
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	320 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	321 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	322
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	323 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	324
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	325 self.f.seek(0)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	326 self.f.write(header)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	327
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	328 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	329 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	330 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	331 if mat_type!='MATRIX':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	332 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	333 self.length = int(l)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	334 self.width = int(w)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	335 if endianness=='LITTLE_ENDIAN':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	336 byteorder = 'little'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	337 elif endianness=='BIG_ENDIAN':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	338 byteorder = 'big'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	339 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	340 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	341 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	342
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	343 if data_type=='DOUBLE':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	344 self.elemtype = 'd'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	345 self.elemsize = 8
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	346 elif data_type=='FLOAT':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	347 self.elemtype = 'f'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	348 self.elemsize = 4
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	349 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	350 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	351 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	352
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	353 def load_fieldnames(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	354 self.fieldnames = []
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	355 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	356 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	357 f = open(fieldnamefile)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	358 for row in f:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	359 row = row.split()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	360 if len(row)>0:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	361 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	362 f.close()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	363 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	364 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	365
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	366 def save_fieldnames(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	367 metadatadir = self.fname+'.metadata'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	368 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	369 os.mkdir(metadatadir)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	370 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	371 f = open(fieldnamefile,'wb')
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	372 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	373 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	374 f.close()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	375
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	376 def getRow(self,i):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	377 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	378 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	379 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	380 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	381 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	382 if self.swap_bytes:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	383 ar.byteswap(True)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	384 return ar
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	385
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	386 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	387 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	388 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	389 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	390 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	391 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	392 if self.swap_bytes:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	393 ar.byteswap(True)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	394 return ar
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	395
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	396 def checkzerorow(self,i):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	397 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	398 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	399 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	400 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	401 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	402 if self.swap_bytes:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	403 ar.byteswap(True)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	404 for elem in ar:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	405 if elem!=0:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	406 return False
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	407 return True
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	408
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	409 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	410 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	411 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	412 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	413 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	414 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	415 raise IndexError
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	416 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	417 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	418 ar.byteswap(True)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	419 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	420 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	421 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	422 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	423
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	424 def appendRow(self,row):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	425 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	426 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	427 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	428 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	429 ar.byteswap(True)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	430 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	431 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	432
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	433 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	434 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	435 self.length += 1
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	436 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	437
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	438 def flush(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	439 self.f.flush()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	440
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	441 def close(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	442 if hasattr(self, 'f'):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	443 self.f.close()
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 def append(self,row):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	446 self.appendRow(row)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	447
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	448 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	449 l = self.length
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	450 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	451 self.putRow(i,row)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	452
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	453 def __len__(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	454 return self.length
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	455
380 c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	456
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	457
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	458 #copied from PLEARNDIR:python_modules/plearn/vmat/readAMat.py
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	459 def safefloat(str):
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	460 """Convert the given string to its float value. It is 'safe' in the sense
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	461 that missing values ('nan') will be properly converted to the corresponding
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	462 float value under all platforms, contrarily to 'float(str)'.
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	463 """
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	464 if str.lower() == 'nan':
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	465 return fpconst.NaN
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	466 else:
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	467 return float(str)
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	468
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	469 #copied from PLEARNDIR:python_modules/plearn/vmat/readAMat.py
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	470 def readAMat(amatname):
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	471 """Read a PLearn .amat file and return it as a numarray Array.
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	472
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	473 Return a tuple, with as the first argument the array itself, and as
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	474 the second argument the fieldnames (list of strings).
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	475 """
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	476 ### NOTE: this version is much faster than first creating the array and
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	477 ### updating each row as it is read... Bizarrely enough
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	478 f = open(amatname)
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	479 a = []
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	480 fieldnames = []
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	481 for line in f:
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	482 if line.startswith("#size:"):
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	483 (length,width) = line[6:].strip().split()
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	484 elif line.startswith("#sizes:"): # ignore input/target/weight/extra sizes
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	485 continue
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	486
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	487 elif line.startswith("#:"):
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	488 fieldnames = line[2:].strip().split()
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	489 pass
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	490 elif not line.startswith('#'):
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	491 # Add all non-comment lines.
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	492 row = [ safefloat(x) for x in line.strip().split() ]
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	493 if row:
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	494 a.append(row)
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	495
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	496 f.close()
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	497 return numpy.numarray.array(a), fieldnames
c2f17f231960 added function to load amat file Frederic Bastien <bastienf@iro.umontreal.ca> parents: 116 diff changeset	498
114 d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	499
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	500 if __name__ == '__main__':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	501 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	502 pmat.append( [1, 2] )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	503 pmat.append( [3, 4] )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	504 pmat.close()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	505
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	506 pmat = PMat( 'tmp.pmat', 'r' )
116 9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	507 ar=load_pmat_as_array('tmp.pmat')
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	508 ds=load_pmat_as_array_dataset('tmp.pmat')
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	509
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	510 print "PMat",pmat
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	511 print "PMat",pmat[:]
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	512 print "array",ar
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	513 print "ArrayDataSet",ds
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	514 for i in ds:
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	515 print i
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	516 save_array_dataset_as_pmat("tmp2.pmat",ds)
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	517 ds2=load_pmat_as_array_dataset('tmp2.pmat')
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	518 for i in ds2:
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	519 print i
114 d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	520 # print "+++ tmp.pmat contains: "
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	521 # os.system( 'plearn vmat cat tmp.pmat' )
116 9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	522 import shutil
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	523 for fname in ["tmp.pmat", "tmp2.pmat"]:
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	524 os.remove( fname )
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	525 if os.path.exists( fname+'.metadata' ):
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	526 shutil.rmtree( fname+'.metadata' )

Mercurial > pylearn

annotate pmat.py @ 421:e01f17be270a