_arff.py
37.9 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
# -*- coding: utf-8 -*-
# =============================================================================
# Federal University of Rio Grande do Sul (UFRGS)
# Connectionist Artificial Intelligence Laboratory (LIAC)
# Renato de Pontes Pereira - rppereira@inf.ufrgs.br
# =============================================================================
# Copyright (c) 2011 Renato de Pontes Pereira, renato.ppontes at gmail dot com
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
# =============================================================================
'''
The liac-arff module implements functions to read and write ARFF files in
Python. It was created in the Connectionist Artificial Intelligence Laboratory
(LIAC), which takes place at the Federal University of Rio Grande do Sul
(UFRGS), in Brazil.
ARFF (Attribute-Relation File Format) is an file format specially created for
describe datasets which are commonly used for machine learning experiments and
softwares. This file format was created to be used in Weka, the best
representative software for machine learning automated experiments.
An ARFF file can be divided into two sections: header and data. The Header
describes the metadata of the dataset, including a general description of the
dataset, its name and its attributes. The source below is an example of a
header section in a XOR dataset::
%
% XOR Dataset
%
% Created by Renato Pereira
% rppereira@inf.ufrgs.br
% http://inf.ufrgs.br/~rppereira
%
%
@RELATION XOR
@ATTRIBUTE input1 REAL
@ATTRIBUTE input2 REAL
@ATTRIBUTE y REAL
The Data section of an ARFF file describes the observations of the dataset, in
the case of XOR dataset::
@DATA
0.0,0.0,0.0
0.0,1.0,1.0
1.0,0.0,1.0
1.0,1.0,0.0
%
%
%
Notice that several lines are starting with an ``%`` symbol, denoting a
comment, thus, lines with ``%`` at the beginning will be ignored, except by the
description part at the beginning of the file. The declarations ``@RELATION``,
``@ATTRIBUTE``, and ``@DATA`` are all case insensitive and obligatory.
For more information and details about the ARFF file description, consult
http://www.cs.waikato.ac.nz/~ml/weka/arff.html
ARFF Files in Python
~~~~~~~~~~~~~~~~~~~~
This module uses built-ins python objects to represent a deserialized ARFF
file. A dictionary is used as the container of the data and metadata of ARFF,
and have the following keys:
- **description**: (OPTIONAL) a string with the description of the dataset.
- **relation**: (OBLIGATORY) a string with the name of the dataset.
- **attributes**: (OBLIGATORY) a list of attributes with the following
template::
(attribute_name, attribute_type)
the attribute_name is a string, and attribute_type must be an string
or a list of strings.
- **data**: (OBLIGATORY) a list of data instances. Each data instance must be
a list with values, depending on the attributes.
The above keys must follow the case which were described, i.e., the keys are
case sensitive. The attribute type ``attribute_type`` must be one of these
strings (they are not case sensitive): ``NUMERIC``, ``INTEGER``, ``REAL`` or
``STRING``. For nominal attributes, the ``attribute_type`` must be a list of
strings.
In this format, the XOR dataset presented above can be represented as a python
object as::
xor_dataset = {
'description': 'XOR Dataset',
'relation': 'XOR',
'attributes': [
('input1', 'REAL'),
('input2', 'REAL'),
('y', 'REAL'),
],
'data': [
[0.0, 0.0, 0.0],
[0.0, 1.0, 1.0],
[1.0, 0.0, 1.0],
[1.0, 1.0, 0.0]
]
}
Features
~~~~~~~~
This module provides several features, including:
- Read and write ARFF files using python built-in structures, such dictionaries
and lists;
- Supports `scipy.sparse.coo <http://docs.scipy
.org/doc/scipy/reference/generated/scipy.sparse.coo_matrix.html#scipy.sparse.coo_matrix>`_
and lists of dictionaries as used by SVMLight
- Supports the following attribute types: NUMERIC, REAL, INTEGER, STRING, and
NOMINAL;
- Has an interface similar to other built-in modules such as ``json``, or
``zipfile``;
- Supports read and write the descriptions of files;
- Supports missing values and names with spaces;
- Supports unicode values and names;
- Fully compatible with Python 2.7+, Python 3.3+, pypy and pypy3;
- Under `MIT License <http://opensource.org/licenses/MIT>`_
'''
__author__ = 'Renato de Pontes Pereira, Matthias Feurer, Joel Nothman'
__author_email__ = ('renato.ppontes@gmail.com, '
'feurerm@informatik.uni-freiburg.de, '
'joel.nothman@gmail.com')
__version__ = '2.4.0'
from typing import Optional
import re
import sys
import csv
# CONSTANTS ===================================================================
_SIMPLE_TYPES = ['NUMERIC', 'REAL', 'INTEGER', 'STRING']
_TK_DESCRIPTION = '%'
_TK_COMMENT = '%'
_TK_RELATION = '@RELATION'
_TK_ATTRIBUTE = '@ATTRIBUTE'
_TK_DATA = '@DATA'
_RE_RELATION = re.compile(r'^([^\{\}%,\s]*|\".*\"|\'.*\')$', re.UNICODE)
_RE_ATTRIBUTE = re.compile(r'^(\".*\"|\'.*\'|[^\{\}%,\s]*)\s+(.+)$', re.UNICODE)
_RE_TYPE_NOMINAL = re.compile(r'^\{\s*((\".*\"|\'.*\'|\S*)\s*,\s*)*(\".*\"|\'.*\'|\S*)\s*\}$', re.UNICODE)
_RE_QUOTE_CHARS = re.compile(r'["\'\\\s%,\000-\031]', re.UNICODE)
_RE_ESCAPE_CHARS = re.compile(r'(?=["\'\\%])|[\n\r\t\000-\031]')
_RE_SPARSE_LINE = re.compile(r'^\s*\{.*\}\s*$', re.UNICODE)
_RE_NONTRIVIAL_DATA = re.compile('["\'{}\\s]', re.UNICODE)
def _build_re_values():
quoted_re = r'''
" # open quote followed by zero or more of:
(?:
(?<!\\) # no additional backslash
(?:\\\\)* # maybe escaped backslashes
\\" # escaped quote
|
\\[^"] # escaping a non-quote
|
[^"\\] # non-quote char
)*
" # close quote
'''
# a value is surrounded by " or by ' or contains no quotables
value_re = r'''(?:
%s| # a value may be surrounded by "
%s| # or by '
[^,\s"'{}]+ # or may contain no characters requiring quoting
)''' % (quoted_re,
quoted_re.replace('"', "'"))
# This captures (value, error) groups. Because empty values are allowed,
# we cannot just look for empty values to handle syntax errors.
# We presume the line has had ',' prepended...
dense = re.compile(r'''(?x)
, # may follow ','
\s*
((?=,)|$|%(value_re)s) # empty or value
|
(\S.*) # error
''' % {'value_re': value_re})
# This captures (key, value) groups and will have an empty key/value
# in case of syntax errors.
# It does not ensure that the line starts with '{' or ends with '}'.
sparse = re.compile(r'''(?x)
(?:^\s*\{|,) # may follow ',', or '{' at line start
\s*
(\d+) # attribute key
\s+
(%(value_re)s) # value
|
(?!}\s*$) # not an error if it's }$
(?!^\s*{\s*}\s*$) # not an error if it's ^{}$
\S.* # error
''' % {'value_re': value_re})
return dense, sparse
_RE_DENSE_VALUES, _RE_SPARSE_KEY_VALUES = _build_re_values()
_ESCAPE_SUB_MAP = {
'\\\\': '\\',
'\\"': '"',
"\\'": "'",
'\\t': '\t',
'\\n': '\n',
'\\r': '\r',
'\\b': '\b',
'\\f': '\f',
'\\%': '%',
}
_UNESCAPE_SUB_MAP = {chr(i): '\\%03o' % i for i in range(32)}
_UNESCAPE_SUB_MAP.update({v: k for k, v in _ESCAPE_SUB_MAP.items()})
_UNESCAPE_SUB_MAP[''] = '\\'
_ESCAPE_SUB_MAP.update({'\\%d' % i: chr(i) for i in range(10)})
def _escape_sub_callback(match):
s = match.group()
if len(s) == 2:
try:
return _ESCAPE_SUB_MAP[s]
except KeyError:
raise ValueError('Unsupported escape sequence: %s' % s)
if s[1] == 'u':
return unichr(int(s[2:], 16))
else:
return chr(int(s[1:], 8))
def _unquote(v):
if v[:1] in ('"', "'"):
return re.sub(r'\\([0-9]{1,3}|u[0-9a-f]{4}|.)', _escape_sub_callback,
v[1:-1])
elif v in ('?', ''):
return None
else:
return v
def _parse_values(s):
'''(INTERNAL) Split a line into a list of values'''
if not _RE_NONTRIVIAL_DATA.search(s):
# Fast path for trivial cases (unfortunately we have to handle missing
# values because of the empty string case :(.)
return [None if s in ('?', '') else s
for s in next(csv.reader([s]))]
# _RE_DENSE_VALUES tokenizes despite quoting, whitespace, etc.
values, errors = zip(*_RE_DENSE_VALUES.findall(',' + s))
if not any(errors):
return [_unquote(v) for v in values]
if _RE_SPARSE_LINE.match(s):
try:
return {int(k): _unquote(v)
for k, v in _RE_SPARSE_KEY_VALUES.findall(s)}
except ValueError as exc:
# an ARFF syntax error in sparse data
for match in _RE_SPARSE_KEY_VALUES.finditer(s):
if not match.group(1):
raise BadLayout('Error parsing %r' % match.group())
raise BadLayout('Unknown parsing error')
else:
# an ARFF syntax error
for match in _RE_DENSE_VALUES.finditer(s):
if match.group(2):
raise BadLayout('Error parsing %r' % match.group())
raise BadLayout('Unknown parsing error')
DENSE = 0 # Constant value representing a dense matrix
COO = 1 # Constant value representing a sparse matrix in coordinate format
LOD = 2 # Constant value representing a sparse matrix in list of
# dictionaries format
DENSE_GEN = 3 # Generator of dictionaries
LOD_GEN = 4 # Generator of dictionaries
_SUPPORTED_DATA_STRUCTURES = [DENSE, COO, LOD, DENSE_GEN, LOD_GEN]
# =============================================================================
# COMPATIBILITY WITH PYTHON 3 =================================================
PY3 = sys.version_info[0] == 3
if PY3:
unicode = str
basestring = str
xrange = range
unichr = chr
# COMPABILITY WITH PYTHON 2 ===================================================
# =============================================================================
PY2 = sys.version_info[0] == 2
if PY2:
from itertools import izip as zip
# EXCEPTIONS ==================================================================
class ArffException(Exception):
message : Optional[str] = None
def __init__(self):
self.line = -1
def __str__(self):
return self.message%self.line
class BadRelationFormat(ArffException):
'''Error raised when the relation declaration is in an invalid format.'''
message = 'Bad @RELATION format, at line %d.'
class BadAttributeFormat(ArffException):
'''Error raised when some attribute declaration is in an invalid format.'''
message = 'Bad @ATTRIBUTE format, at line %d.'
class BadDataFormat(ArffException):
'''Error raised when some data instance is in an invalid format.'''
def __init__(self, value):
super(BadDataFormat, self).__init__()
self.message = (
'Bad @DATA instance format in line %d: ' +
('%s' % value)
)
class BadAttributeType(ArffException):
'''Error raised when some invalid type is provided into the attribute
declaration.'''
message = 'Bad @ATTRIBUTE type, at line %d.'
class BadAttributeName(ArffException):
'''Error raised when an attribute name is provided twice the attribute
declaration.'''
def __init__(self, value, value2):
super(BadAttributeName, self).__init__()
self.message = (
('Bad @ATTRIBUTE name %s at line' % value) +
' %d, this name is already in use in line' +
(' %d.' % value2)
)
class BadNominalValue(ArffException):
'''Error raised when a value in used in some data instance but is not
declared into it respective attribute declaration.'''
def __init__(self, value):
super(BadNominalValue, self).__init__()
self.message = (
('Data value %s not found in nominal declaration, ' % value)
+ 'at line %d.'
)
class BadNominalFormatting(ArffException):
'''Error raised when a nominal value with space is not properly quoted.'''
def __init__(self, value):
super(BadNominalFormatting, self).__init__()
self.message = (
('Nominal data value "%s" not properly quoted in line ' % value) +
'%d.'
)
class BadNumericalValue(ArffException):
'''Error raised when and invalid numerical value is used in some data
instance.'''
message = 'Invalid numerical value, at line %d.'
class BadStringValue(ArffException):
'''Error raise when a string contains space but is not quoted.'''
message = 'Invalid string value at line %d.'
class BadLayout(ArffException):
'''Error raised when the layout of the ARFF file has something wrong.'''
message = 'Invalid layout of the ARFF file, at line %d.'
def __init__(self, msg=''):
super(BadLayout, self).__init__()
if msg:
self.message = BadLayout.message + ' ' + msg.replace('%', '%%')
class BadObject(ArffException):
'''Error raised when the object representing the ARFF file has something
wrong.'''
def __init__(self, msg='Invalid object.'):
self.msg = msg
def __str__(self):
return '%s' % self.msg
# =============================================================================
# INTERNAL ====================================================================
def _unescape_sub_callback(match):
return _UNESCAPE_SUB_MAP[match.group()]
def encode_string(s):
if _RE_QUOTE_CHARS.search(s):
return u"'%s'" % _RE_ESCAPE_CHARS.sub(_unescape_sub_callback, s)
return s
class EncodedNominalConversor(object):
def __init__(self, values):
self.values = {v: i for i, v in enumerate(values)}
self.values[0] = 0
def __call__(self, value):
try:
return self.values[value]
except KeyError:
raise BadNominalValue(value)
class NominalConversor(object):
def __init__(self, values):
self.values = set(values)
self.zero_value = values[0]
def __call__(self, value):
if value not in self.values:
if value == 0:
# Sparse decode
# See issue #52: nominals should take their first value when
# unspecified in a sparse matrix. Naturally, this is consistent
# with EncodedNominalConversor.
return self.zero_value
raise BadNominalValue(value)
return unicode(value)
class DenseGeneratorData(object):
'''Internal helper class to allow for different matrix types without
making the code a huge collection of if statements.'''
def decode_rows(self, stream, conversors):
for row in stream:
values = _parse_values(row)
if isinstance(values, dict):
if values and max(values) >= len(conversors):
raise BadDataFormat(row)
# XXX: int 0 is used for implicit values, not '0'
values = [values[i] if i in values else 0 for i in
xrange(len(conversors))]
else:
if len(values) != len(conversors):
raise BadDataFormat(row)
yield self._decode_values(values, conversors)
@staticmethod
def _decode_values(values, conversors):
try:
values = [None if value is None else conversor(value)
for conversor, value
in zip(conversors, values)]
except ValueError as exc:
if 'float: ' in str(exc):
raise BadNumericalValue()
return values
def encode_data(self, data, attributes):
'''(INTERNAL) Encodes a line of data.
Data instances follow the csv format, i.e, attribute values are
delimited by commas. After converted from csv.
:param data: a list of values.
:param attributes: a list of attributes. Used to check if data is valid.
:return: a string with the encoded data line.
'''
current_row = 0
for inst in data:
if len(inst) != len(attributes):
raise BadObject(
'Instance %d has %d attributes, expected %d' %
(current_row, len(inst), len(attributes))
)
new_data = []
for value in inst:
if value is None or value == u'' or value != value:
s = '?'
else:
s = encode_string(unicode(value))
new_data.append(s)
current_row += 1
yield u','.join(new_data)
class _DataListMixin(object):
"""Mixin to return a list from decode_rows instead of a generator"""
def decode_rows(self, stream, conversors):
return list(super(_DataListMixin, self).decode_rows(stream, conversors))
class Data(_DataListMixin, DenseGeneratorData):
pass
class COOData(object):
def decode_rows(self, stream, conversors):
data, rows, cols = [], [], []
for i, row in enumerate(stream):
values = _parse_values(row)
if not isinstance(values, dict):
raise BadLayout()
if not values:
continue
row_cols, values = zip(*sorted(values.items()))
try:
values = [value if value is None else conversors[key](value)
for key, value in zip(row_cols, values)]
except ValueError as exc:
if 'float: ' in str(exc):
raise BadNumericalValue()
raise
except IndexError:
# conversor out of range
raise BadDataFormat(row)
data.extend(values)
rows.extend([i] * len(values))
cols.extend(row_cols)
return data, rows, cols
def encode_data(self, data, attributes):
num_attributes = len(attributes)
new_data = []
current_row = 0
row = data.row
col = data.col
data = data.data
# Check if the rows are sorted
if not all(row[i] <= row[i + 1] for i in xrange(len(row) - 1)):
raise ValueError("liac-arff can only output COO matrices with "
"sorted rows.")
for v, col, row in zip(data, col, row):
if row > current_row:
# Add empty rows if necessary
while current_row < row:
yield " ".join([u"{", u','.join(new_data), u"}"])
new_data = []
current_row += 1
if col >= num_attributes:
raise BadObject(
'Instance %d has at least %d attributes, expected %d' %
(current_row, col + 1, num_attributes)
)
if v is None or v == u'' or v != v:
s = '?'
else:
s = encode_string(unicode(v))
new_data.append("%d %s" % (col, s))
yield " ".join([u"{", u','.join(new_data), u"}"])
class LODGeneratorData(object):
def decode_rows(self, stream, conversors):
for row in stream:
values = _parse_values(row)
if not isinstance(values, dict):
raise BadLayout()
try:
yield {key: None if value is None else conversors[key](value)
for key, value in values.items()}
except ValueError as exc:
if 'float: ' in str(exc):
raise BadNumericalValue()
raise
except IndexError:
# conversor out of range
raise BadDataFormat(row)
def encode_data(self, data, attributes):
current_row = 0
num_attributes = len(attributes)
for row in data:
new_data = []
if len(row) > 0 and max(row) >= num_attributes:
raise BadObject(
'Instance %d has %d attributes, expected %d' %
(current_row, max(row) + 1, num_attributes)
)
for col in sorted(row):
v = row[col]
if v is None or v == u'' or v != v:
s = '?'
else:
s = encode_string(unicode(v))
new_data.append("%d %s" % (col, s))
current_row += 1
yield " ".join([u"{", u','.join(new_data), u"}"])
class LODData(_DataListMixin, LODGeneratorData):
pass
def _get_data_object_for_decoding(matrix_type):
if matrix_type == DENSE:
return Data()
elif matrix_type == COO:
return COOData()
elif matrix_type == LOD:
return LODData()
elif matrix_type == DENSE_GEN:
return DenseGeneratorData()
elif matrix_type == LOD_GEN:
return LODGeneratorData()
else:
raise ValueError("Matrix type %s not supported." % str(matrix_type))
def _get_data_object_for_encoding(matrix):
# Probably a scipy.sparse
if hasattr(matrix, 'format'):
if matrix.format == 'coo':
return COOData()
else:
raise ValueError('Cannot guess matrix format!')
elif isinstance(matrix[0], dict):
return LODData()
else:
return Data()
# =============================================================================
# ADVANCED INTERFACE ==========================================================
class ArffDecoder(object):
'''An ARFF decoder.'''
def __init__(self):
'''Constructor.'''
self._conversors = []
self._current_line = 0
def _decode_comment(self, s):
'''(INTERNAL) Decodes a comment line.
Comments are single line strings starting, obligatorily, with the ``%``
character, and can have any symbol, including whitespaces or special
characters.
This method must receive a normalized string, i.e., a string without
padding, including the "\r\n" characters.
:param s: a normalized string.
:return: a string with the decoded comment.
'''
res = re.sub(r'^\%( )?', '', s)
return res
def _decode_relation(self, s):
'''(INTERNAL) Decodes a relation line.
The relation declaration is a line with the format ``@RELATION
<relation-name>``, where ``relation-name`` is a string. The string must
start with alphabetic character and must be quoted if the name includes
spaces, otherwise this method will raise a `BadRelationFormat` exception.
This method must receive a normalized string, i.e., a string without
padding, including the "\r\n" characters.
:param s: a normalized string.
:return: a string with the decoded relation name.
'''
_, v = s.split(' ', 1)
v = v.strip()
if not _RE_RELATION.match(v):
raise BadRelationFormat()
res = unicode(v.strip('"\''))
return res
def _decode_attribute(self, s):
'''(INTERNAL) Decodes an attribute line.
The attribute is the most complex declaration in an arff file. All
attributes must follow the template::
@attribute <attribute-name> <datatype>
where ``attribute-name`` is a string, quoted if the name contains any
whitespace, and ``datatype`` can be:
- Numerical attributes as ``NUMERIC``, ``INTEGER`` or ``REAL``.
- Strings as ``STRING``.
- Dates (NOT IMPLEMENTED).
- Nominal attributes with format:
{<nominal-name1>, <nominal-name2>, <nominal-name3>, ...}
The nominal names follow the rules for the attribute names, i.e., they
must be quoted if the name contains whitespaces.
This method must receive a normalized string, i.e., a string without
padding, including the "\r\n" characters.
:param s: a normalized string.
:return: a tuple (ATTRIBUTE_NAME, TYPE_OR_VALUES).
'''
_, v = s.split(' ', 1)
v = v.strip()
# Verify the general structure of declaration
m = _RE_ATTRIBUTE.match(v)
if not m:
raise BadAttributeFormat()
# Extracts the raw name and type
name, type_ = m.groups()
# Extracts the final name
name = unicode(name.strip('"\''))
# Extracts the final type
if _RE_TYPE_NOMINAL.match(type_):
try:
type_ = _parse_values(type_.strip('{} '))
except Exception:
raise BadAttributeType()
if isinstance(type_, dict):
raise BadAttributeType()
else:
# If not nominal, verify the type name
type_ = unicode(type_).upper()
if type_ not in ['NUMERIC', 'REAL', 'INTEGER', 'STRING']:
raise BadAttributeType()
return (name, type_)
def _decode(self, s, encode_nominal=False, matrix_type=DENSE):
'''Do the job the ``encode``.'''
# Make sure this method is idempotent
self._current_line = 0
# If string, convert to a list of lines
if isinstance(s, basestring):
s = s.strip('\r\n ').replace('\r\n', '\n').split('\n')
# Create the return object
obj = {
u'description': u'',
u'relation': u'',
u'attributes': [],
u'data': []
}
attribute_names = {}
# Create the data helper object
data = _get_data_object_for_decoding(matrix_type)
# Read all lines
STATE = _TK_DESCRIPTION
s = iter(s)
for row in s:
self._current_line += 1
# Ignore empty lines
row = row.strip(' \r\n')
if not row: continue
u_row = row.upper()
# DESCRIPTION -----------------------------------------------------
if u_row.startswith(_TK_DESCRIPTION) and STATE == _TK_DESCRIPTION:
obj['description'] += self._decode_comment(row) + '\n'
# -----------------------------------------------------------------
# RELATION --------------------------------------------------------
elif u_row.startswith(_TK_RELATION):
if STATE != _TK_DESCRIPTION:
raise BadLayout()
STATE = _TK_RELATION
obj['relation'] = self._decode_relation(row)
# -----------------------------------------------------------------
# ATTRIBUTE -------------------------------------------------------
elif u_row.startswith(_TK_ATTRIBUTE):
if STATE != _TK_RELATION and STATE != _TK_ATTRIBUTE:
raise BadLayout()
STATE = _TK_ATTRIBUTE
attr = self._decode_attribute(row)
if attr[0] in attribute_names:
raise BadAttributeName(attr[0], attribute_names[attr[0]])
else:
attribute_names[attr[0]] = self._current_line
obj['attributes'].append(attr)
if isinstance(attr[1], (list, tuple)):
if encode_nominal:
conversor = EncodedNominalConversor(attr[1])
else:
conversor = NominalConversor(attr[1])
else:
CONVERSOR_MAP = {'STRING': unicode,
'INTEGER': lambda x: int(float(x)),
'NUMERIC': float,
'REAL': float}
conversor = CONVERSOR_MAP[attr[1]]
self._conversors.append(conversor)
# -----------------------------------------------------------------
# DATA ------------------------------------------------------------
elif u_row.startswith(_TK_DATA):
if STATE != _TK_ATTRIBUTE:
raise BadLayout()
break
# -----------------------------------------------------------------
# COMMENT ---------------------------------------------------------
elif u_row.startswith(_TK_COMMENT):
pass
# -----------------------------------------------------------------
else:
# Never found @DATA
raise BadLayout()
def stream():
for row in s:
self._current_line += 1
row = row.strip()
# Ignore empty lines and comment lines.
if row and not row.startswith(_TK_COMMENT):
yield row
# Alter the data object
obj['data'] = data.decode_rows(stream(), self._conversors)
if obj['description'].endswith('\n'):
obj['description'] = obj['description'][:-1]
return obj
def decode(self, s, encode_nominal=False, return_type=DENSE):
'''Returns the Python representation of a given ARFF file.
When a file object is passed as an argument, this method reads lines
iteratively, avoiding to load unnecessary information to the memory.
:param s: a string or file object with the ARFF file.
:param encode_nominal: boolean, if True perform a label encoding
while reading the .arff file.
:param return_type: determines the data structure used to store the
dataset. Can be one of `arff.DENSE`, `arff.COO`, `arff.LOD`,
`arff.DENSE_GEN` or `arff.LOD_GEN`.
Consult the sections on `working with sparse data`_ and `loading
progressively`_.
'''
try:
return self._decode(s, encode_nominal=encode_nominal,
matrix_type=return_type)
except ArffException as e:
e.line = self._current_line
raise e
class ArffEncoder(object):
'''An ARFF encoder.'''
def _encode_comment(self, s=''):
'''(INTERNAL) Encodes a comment line.
Comments are single line strings starting, obligatorily, with the ``%``
character, and can have any symbol, including whitespaces or special
characters.
If ``s`` is None, this method will simply return an empty comment.
:param s: (OPTIONAL) string.
:return: a string with the encoded comment line.
'''
if s:
return u'%s %s'%(_TK_COMMENT, s)
else:
return u'%s' % _TK_COMMENT
def _encode_relation(self, name):
'''(INTERNAL) Decodes a relation line.
The relation declaration is a line with the format ``@RELATION
<relation-name>``, where ``relation-name`` is a string.
:param name: a string.
:return: a string with the encoded relation declaration.
'''
for char in ' %{},':
if char in name:
name = '"%s"'%name
break
return u'%s %s'%(_TK_RELATION, name)
def _encode_attribute(self, name, type_):
'''(INTERNAL) Encodes an attribute line.
The attribute follow the template::
@attribute <attribute-name> <datatype>
where ``attribute-name`` is a string, and ``datatype`` can be:
- Numerical attributes as ``NUMERIC``, ``INTEGER`` or ``REAL``.
- Strings as ``STRING``.
- Dates (NOT IMPLEMENTED).
- Nominal attributes with format:
{<nominal-name1>, <nominal-name2>, <nominal-name3>, ...}
This method must receive a the name of the attribute and its type, if
the attribute type is nominal, ``type`` must be a list of values.
:param name: a string.
:param type_: a string or a list of string.
:return: a string with the encoded attribute declaration.
'''
for char in ' %{},':
if char in name:
name = '"%s"'%name
break
if isinstance(type_, (tuple, list)):
type_tmp = [u'%s' % encode_string(type_k) for type_k in type_]
type_ = u'{%s}'%(u', '.join(type_tmp))
return u'%s %s %s'%(_TK_ATTRIBUTE, name, type_)
def encode(self, obj):
'''Encodes a given object to an ARFF file.
:param obj: the object containing the ARFF information.
:return: the ARFF file as an unicode string.
'''
data = [row for row in self.iter_encode(obj)]
return u'\n'.join(data)
def iter_encode(self, obj):
'''The iterative version of `arff.ArffEncoder.encode`.
This encodes iteratively a given object and return, one-by-one, the
lines of the ARFF file.
:param obj: the object containing the ARFF information.
:return: (yields) the ARFF file as unicode strings.
'''
# DESCRIPTION
if obj.get('description', None):
for row in obj['description'].split('\n'):
yield self._encode_comment(row)
# RELATION
if not obj.get('relation'):
raise BadObject('Relation name not found or with invalid value.')
yield self._encode_relation(obj['relation'])
yield u''
# ATTRIBUTES
if not obj.get('attributes'):
raise BadObject('Attributes not found.')
attribute_names = set()
for attr in obj['attributes']:
# Verify for bad object format
if not isinstance(attr, (tuple, list)) or \
len(attr) != 2 or \
not isinstance(attr[0], basestring):
raise BadObject('Invalid attribute declaration "%s"'%str(attr))
if isinstance(attr[1], basestring):
# Verify for invalid types
if attr[1] not in _SIMPLE_TYPES:
raise BadObject('Invalid attribute type "%s"'%str(attr))
# Verify for bad object format
elif not isinstance(attr[1], (tuple, list)):
raise BadObject('Invalid attribute type "%s"'%str(attr))
# Verify attribute name is not used twice
if attr[0] in attribute_names:
raise BadObject('Trying to use attribute name "%s" for the '
'second time.' % str(attr[0]))
else:
attribute_names.add(attr[0])
yield self._encode_attribute(attr[0], attr[1])
yield u''
attributes = obj['attributes']
# DATA
yield _TK_DATA
if 'data' in obj:
data = _get_data_object_for_encoding(obj.get('data'))
for line in data.encode_data(obj.get('data'), attributes):
yield line
yield u''
# =============================================================================
# BASIC INTERFACE =============================================================
def load(fp, encode_nominal=False, return_type=DENSE):
'''Load a file-like object containing the ARFF document and convert it into
a Python object.
:param fp: a file-like object.
:param encode_nominal: boolean, if True perform a label encoding
while reading the .arff file.
:param return_type: determines the data structure used to store the
dataset. Can be one of `arff.DENSE`, `arff.COO`, `arff.LOD`,
`arff.DENSE_GEN` or `arff.LOD_GEN`.
Consult the sections on `working with sparse data`_ and `loading
progressively`_.
:return: a dictionary.
'''
decoder = ArffDecoder()
return decoder.decode(fp, encode_nominal=encode_nominal,
return_type=return_type)
def loads(s, encode_nominal=False, return_type=DENSE):
'''Convert a string instance containing the ARFF document into a Python
object.
:param s: a string object.
:param encode_nominal: boolean, if True perform a label encoding
while reading the .arff file.
:param return_type: determines the data structure used to store the
dataset. Can be one of `arff.DENSE`, `arff.COO`, `arff.LOD`,
`arff.DENSE_GEN` or `arff.LOD_GEN`.
Consult the sections on `working with sparse data`_ and `loading
progressively`_.
:return: a dictionary.
'''
decoder = ArffDecoder()
return decoder.decode(s, encode_nominal=encode_nominal,
return_type=return_type)
def dump(obj, fp):
'''Serialize an object representing the ARFF document to a given file-like
object.
:param obj: a dictionary.
:param fp: a file-like object.
'''
encoder = ArffEncoder()
generator = encoder.iter_encode(obj)
last_row = next(generator)
for row in generator:
fp.write(last_row + u'\n')
last_row = row
fp.write(last_row)
return fp
def dumps(obj):
'''Serialize an object representing the ARFF document, returning a string.
:param obj: a dictionary.
:return: a string with the ARFF document.
'''
encoder = ArffEncoder()
return encoder.encode(obj)
# =============================================================================