pylearn: pmat.py annotate

annotate pmat.py @ 336:0ce6e62ac6e5

Automated merge with ssh://projects@lgcm.iro.umontreal.ca/hg/pylearn

author	Frederic Bastien <bastienf@iro.umontreal.ca>
date	Mon, 16 Jun 2008 17:07:44 -0400
parents	9330d941fa1f
children	c2f17f231960

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
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	39
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	40 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	41 indices = None
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	42 if isinstance( cols, int ):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	43 indices = [ cols ]
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	44 elif isinstance( cols, slice ):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	45 #print cols
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	46 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	47 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	48 indices = list( cols )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	49
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	50 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	51
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	52 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	53 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	54 formatstr = s[0:64]
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	55 datastr = s[64:]
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	56 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	57
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	58 if data_type=='DOUBLE':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	59 elemtype = 'd'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	60 elif data_type=='FLOAT':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	61 elemtype = 'f'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	62 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	63 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	64
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	65 if endianness=='LITTLE_ENDIAN':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	66 byteorder = 'little'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	67 elif endianness=='BIG_ENDIAN':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	68 byteorder = 'big'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	69 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	70 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	71
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	72 l = int(l)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	73 w = int(w)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	74 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	75 if byteorder!=sys.byteorder:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	76 X.byteswap(True)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	77 return X
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	78
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	79 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	80 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	81
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 #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	83 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	84
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 #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	86 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 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	88 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	89 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	90 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	91 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	92 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	93 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	94 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	95 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	96 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	97
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 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	99
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 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	101 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	102 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	103
114 d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	104 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	105 s = file(fname,'wb')
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	106
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	107 length, width = ar.shape
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	108 if fieldnames:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	109 assert len(fieldnames) == width
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	110 metadatadir = fname+'.metadata'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	111 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	112 os.mkdir(metadatadir)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	113 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	114 f = open(fieldnamefile,'wb')
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	115 for name in fieldnames:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	116 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	117 f.close()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	118
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	119 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	120 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	121 header += 'DOUBLE '
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	122 elemsize = 8
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	123
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	124 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	125 header += 'FLOAT '
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	126 elemsize = 4
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 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	129 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	130
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	131 rowsize = elemsize*width
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	132
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	133 if sys.byteorder=='little':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	134 header += 'LITTLE_ENDIAN '
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	135 elif sys.byteorder=='big':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	136 header += 'BIG_ENDIAN '
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	137 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	138 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	139
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	140 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	141 s.write( header )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	142 s.write( ar.tostring() )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	143 s.close()
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
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	146 ####### Iterators ###########################################################
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	147
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	148 class VMatIt:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	149 def __init__(self, vmat):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	150 self.vmat = vmat
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	151 self.cur_row = 0
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 def __iter__(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	154 return self
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	155
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	156 def next(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	157 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	158 raise StopIteration
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	159 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	160 self.cur_row += 1
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	161 return row
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 ColumnIt:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	164 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	165 self.vmat = vmat
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	166 self.col = col
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	167 self.cur_row = 0
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 __iter__(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	170 return self
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	171
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	172 def next(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	173 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	174 raise StopIteration
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	175 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	176 self.cur_row += 1
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	177 return val
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	178
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	179 ####### VMat classes ########################################################
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	180
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	181 class VMat:
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 VMatIt(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 __getitem__( self, key ):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	186 if isinstance( key, slice ):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	187 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	188 if step!=None:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	189 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	190
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	191 if start is None:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	192 start = 0
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 l = self.length
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	195 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	196 stop = l
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 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	199
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	200 elif isinstance( key, tuple ):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	201 # Basically returns a SubVMatrix
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	202 assert len(key) == 2
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	203 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	204
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	205 shape = rows.shape
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	206 if len(shape) == 1:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	207 return rows[ key[1] ]
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	208
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	209 cols = key[1]
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	210 if isinstance(cols, slice):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	211 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	212 if start is None:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	213 start = 0
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	214
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	215 if stop is None:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	216 stop = self.width
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	217 elif stop < 0:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	218 stop = self.width+stop
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	219
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	220 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	221
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	222 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	223
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	224 elif isinstance( key, str ):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	225 # 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	226 # returned.
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	227 try:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	228 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	229 self.fieldnames.index(key) )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	230 except ValueError:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	231 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	232 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	233 raise
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 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	236 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	237 return self.getRow(key)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	238
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	239 def getFieldIndex(self, fieldname):
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 self.fieldnames.index(fieldname)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	242 except ValueError:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	243 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	244 %(fieldname, ','.join(self.fieldnames)) )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	245
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	246 class PMat( VMat ):
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 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	249 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	250 self.fname = fname
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	251 self.inputsize = inputsize
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	252 self.targetsize = targetsize
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	253 self.weightsize = weightsize
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	254 if openmode=='r':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	255 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	256 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	257 self.load_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 elif openmode=='w':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	260 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	261 self.fieldnames = fieldnames
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	262 self.save_fieldnames()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	263 self.length = 0
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	264 self.width = len(fieldnames)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	265 self.elemtype = elemtype
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	266 self.swap_bytes = False
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	267 self.write_header()
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 elif openmode=='a':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	270 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	271 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	272 self.load_fieldnames()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	273
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	274 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	275 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	276
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	277 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	278 shape = array.shape
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	279 if len(shape) == 1:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	280 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	281 elif len(shape) == 2:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	282 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	283
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	284 for row in array:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	285 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	286
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	287 def __del__(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	288 self.close()
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 def write_header(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	291 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	292
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	293 if self.elemtype=='d':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	294 header += 'DOUBLE '
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	295 self.elemsize = 8
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	296 elif self.elemtype=='f':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	297 header += 'FLOAT '
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	298 self.elemsize = 4
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	299 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	300 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	301 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	302
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	303 if sys.byteorder=='little':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	304 header += 'LITTLE_ENDIAN '
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	305 elif sys.byteorder=='big':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	306 header += 'BIG_ENDIAN '
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	307 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	308 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	309
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	310 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	311
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	312 self.f.seek(0)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	313 self.f.write(header)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	314
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	315 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	316 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	317 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	318 if mat_type!='MATRIX':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	319 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	320 self.length = int(l)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	321 self.width = int(w)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	322 if endianness=='LITTLE_ENDIAN':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	323 byteorder = 'little'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	324 elif endianness=='BIG_ENDIAN':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	325 byteorder = 'big'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	326 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	327 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	328 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	329
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	330 if data_type=='DOUBLE':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	331 self.elemtype = 'd'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	332 self.elemsize = 8
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	333 elif data_type=='FLOAT':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	334 self.elemtype = 'f'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	335 self.elemsize = 4
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	336 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	337 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	338 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	339
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	340 def load_fieldnames(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	341 self.fieldnames = []
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	342 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	343 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	344 f = open(fieldnamefile)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	345 for row in f:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	346 row = row.split()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	347 if len(row)>0:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	348 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	349 f.close()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	350 else:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	351 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	352
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	353 def save_fieldnames(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	354 metadatadir = self.fname+'.metadata'
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	355 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	356 os.mkdir(metadatadir)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	357 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	358 f = open(fieldnamefile,'wb')
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	359 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	360 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	361 f.close()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	362
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	363 def getRow(self,i):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	364 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	365 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	366 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	367 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	368 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	369 if self.swap_bytes:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	370 ar.byteswap(True)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	371 return ar
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	372
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	373 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	374 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	375 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	376 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	377 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	378 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	379 if self.swap_bytes:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	380 ar.byteswap(True)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	381 return ar
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	382
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	383 def checkzerorow(self,i):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	384 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	385 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	386 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	387 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	388 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	389 if self.swap_bytes:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	390 ar.byteswap(True)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	391 for elem in ar:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	392 if elem!=0:
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	393 return False
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	394 return True
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 putRow(self,i,row):
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 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	400 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	401 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	402 raise IndexError
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	403 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	404 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	405 ar.byteswap(True)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	406 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	407 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	408 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	409 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	410
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	411 def appendRow(self,row):
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 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	415 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	416 ar.byteswap(True)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	417 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	418 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	419
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	420 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	421 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	422 self.length += 1
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	423 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	424
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	425 def flush(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	426 self.f.flush()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	427
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	428 def close(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	429 if hasattr(self, 'f'):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	430 self.f.close()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	431
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	432 def append(self,row):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	433 self.appendRow(row)
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 __setitem__(self, i, row):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	436 l = self.length
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	437 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	438 self.putRow(i,row)
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	439
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	440 def __len__(self):
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	441 return self.length
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	442
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	443
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	444 if __name__ == '__main__':
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	445 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	446 pmat.append( [1, 2] )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	447 pmat.append( [3, 4] )
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	448 pmat.close()
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	449
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	450 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	451 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	452 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	453
9330d941fa1f added function load_pmat_as_array_dataset and save_array_dataset_as_pmat Frederic Bastien <bastienf@iro.umontreal.ca> parents: 115 diff changeset	454 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	455 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	456 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	457 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	458 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	459 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	460 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	461 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	462 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	463 print i
114 d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	464 # print "+++ tmp.pmat contains: "
d6d42a0c1275 file copied from PLearn/python_modules/plearn/vmat/PMat.py Frederic Bastien <bastienf@iro.umontreal.ca> parents: diff changeset	465 # 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	466 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	467 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	468 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	469 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	470 shutil.rmtree( fname+'.metadata' )

Mercurial > pylearn

annotate pmat.py @ 336:0ce6e62ac6e5