# -*- 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 `_ 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 `_ ''' __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 TYPE_CHECKING from typing import Optional, List, Dict, Any, Iterator, Union, Tuple 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) ArffDenseDataType = Iterator[List] ArffSparseDataType = Tuple[List, ...] if TYPE_CHECKING: # typing_extensions is available when mypy is installed from typing_extensions import TypedDict class ArffContainerType(TypedDict): description: str relation: str attributes: List data: Union[ArffDenseDataType, ArffSparseDataType] else: ArffContainerType = Dict[str, Any] def _build_re_values(): quoted_re = r''' " # open quote followed by zero or more of: (?: (?= 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 from exc 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 from exc raise except IndexError as e: # conversor out of range raise BadDataFormat(row) from e 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 from exc raise except IndexError as e: # conversor out of range raise BadDataFormat(row) from e 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 ``, 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 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: {, , , ...} 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 as e: raise BadAttributeType from e 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: ArffContainerType = { 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 ``, 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 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: {, , , ...} 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) # =============================================================================