python/arff.py0000644000175200017530000002137311116205763012706 0ustar mikiomikio# Copyright (c) 2008, Mikio L. Braun, Cheng Soon Ong, Soeren Sonnenburg # All rights reserved. # # Redistribution and use in source and binary forms, with or without # modification, are permitted provided that the following conditions are # met: # # * Redistributions of source code must retain the above copyright # notice, this list of conditions and the following disclaimer. # * Redistributions in binary form must reproduce the above # copyright notice, this list of conditions and the following disclaimer # in the documentation and/or other materials provided with the # distribution. # * Neither the names of the Technical University of Berlin, ETH # Zürich, or Fraunhofer FIRST nor the names of its contributors may be # used to endorse or promote products derived from this software without # specific prior written permission. # # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS # "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT # LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR # A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT # OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, # SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT # LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, # DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY # THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. import re import sys class ArffFile(object): """An ARFF File object describes a data set consisting of a number of data points made up of attributes. The whole data set is called a 'relation'. Supported attributes are: - 'numeric': floating point numbers - 'string': strings - 'nominal': taking one of a number of possible values Not all features of ARFF files are supported yet. The most notable exceptions are: - no sparse data - no support for date and relational attributes Also, parsing of strings might still be a bit brittle. You can either load or save from files, or write and parse from a string. You can also construct an empty ARFF file and then fill in your data by hand. To define attributes use the define_attribute method. Attributes are: - 'relation': name of the relation - 'attributes': names of the attributes - 'attribute_types': types of the attributes - 'attribute_data': additional data, for example for nominal attributes. - 'comment': the initial comment in the file. Typically contains some information on the data set. - 'data': the actual data, by data points. """ def __init__(self): """Construct an empty ARFF structure.""" self.relation = '' self.attributes = [] self.attribute_types = dict() self.attribute_data = dict() self.comment = [] self.data = [] pass @staticmethod def load(filename): """Load an ARFF File from a file.""" o = open(filename) s = o.read() a = ArffFile.parse(s) o.close() return a @staticmethod def parse(s): """Parse an ARFF File already loaded into a string.""" a = ArffFile() a.state = 'comment' a.lineno = 1 for l in s.splitlines(): a.parseline(l) a.lineno += 1 return a def save(self, filename): """Save an arff structure to a file.""" o = open(filename, 'w') o.write(self.write()) o.close() def write(self): """Write an arff structure to a string.""" o = [] print self.comment o.append('% ' + re.sub("\n", "\n% ", self.comment)) o.append("@relation " + self.esc(self.relation)) for a in self.attributes: at = self.attribute_types[a] if at == 'numeric': o.append("@attribute " + self.esc(a) + " numeric") elif at == 'string': o.append("@attribute " + self.esc(a) + " string") elif at == 'nominal': o.append("@attribute " + self.esc(a) + " {" + ','.join(self.attribute_data[a]) + "}") else: raise "Type " + at + " not supported for writing!" o.append("\n@data") for d in self.data: line = [] for e, a in zip(d, self.attributes): at = self.attribute_types[a] if at == 'numeric': line.append(str(e)) elif at == 'string': line.append(esc(e)) elif at == 'nominal': line.append(e) else: raise "Type " + at + " not supported for writing!" o.append(','.join(line)) return "\n".join(o) + "\n" def esc(self, s): "Escape a string if it contains spaces" if re.match(r'\s', s): return "\'" + s + "\'" else: return s def define_attribute(self, name, atype, data=None): """Define a new attribute. atype has to be one of 'numeric', 'string', and 'nominal'. For nominal attributes, pass the possible values as data.""" self.attributes.append(name) self.attribute_types[name] = atype self.attribute_data[name] = data def __parseline(self, l): if self.state == 'comment': if len(l) > 0 and l[0] == '%': self.comment.append(l[2:]) else: self.comment = '\n'.join(self.comment) self.state = 'in_header' self.__parseline(l) elif self.state == 'in_header': ll = l.lower() if ll.startswith('@relation '): self.__parse_relation(l) if ll.startswith('@attribute '): self.__parse_attribute(l) if ll.startswith('@data'): self.state = 'data' elif self.state == 'data': if len(l) > 0 and l[0] != '%': self.__parse_data(l) def __parse_relation(self, l): l = l.split() self.relation = l[1] def __parse_attribute(self, l): p = re.compile(r'[a-zA-Z_][a-zA-Z0-9_]*|\{[^\}]+\}|\'[^\']+\'|\"[^\"]+\"') l = [s.strip() for s in p.findall(l)] name = l[1] atype = l[2].lower() if (atype == 'real' or atype == 'numeric' or atype == 'integer'): self.define_attribute(name, 'numeric') elif atype == 'string': self.define_attribute(name, 'string') elif atype[0] == '{' and atype[-1] == '}': values = [s.strip () for s in atype[1:-1].split(',')] self.define_attribute(name, 'nominal', values) else: print "Unsupported type " + atype + " for attribute " + name + "." def __parse_data(self, l): l = [s.strip() for s in l.split(',')] if len(l) != len(self.attributes): print "Warning: line %d contains wrong number of values" % self.lineno return datum = [] for n, v in zip(self.attributes, l): at = self.attribute_types[n] if at == 'numeric': if re.match(r'[+-]?[0-9]+(?:\.[0-9]*(?:[eE]-?[0-9]+)?)?', v): datum.append(float(v)) else: self.__print_warning('non-numeric value %s for numeric attribute %s' % (v, n)) return elif at == 'string': datum.append(v) elif at == 'nominal': if v in self.attribute_data[n]: datum.append(v) else: self.__print_warning('incorrect value %s for nomial attribute %s' % (v, n)) return self.data.append(datum) def __print_warning(self, msg): print ('Warning (line %d): ' % self.lineno) + msg def dump(self): """Print an overview of the ARFF file.""" print "Relation " + self.relation print " With attributes" for n in self.attributes: if self.attribute_types[n] != 'nominal': print " %s of type %s" % (n, self.attribute_types[n]) else: print (" " + n + " of type nominal with values " + ', '.join(self.attribute_data[n])) for d in self.data: print d #a = ArffFile.read('../examples/diabetes.arff') if __name__ == '__main__': a = ArffFile.parse("""% yes % this is great @relation foobar @attribute foo {a,b,c} @attribute bar real @data a, 1 b, 2 c, d d, 3 """) a.dump() print a.write() ruby/arff.rb0000644000175200017530000002157511116205724012322 0ustar mikiomikio# Code to load/write ARFF-files # # Copyright (c) 2008, Mikio L. Braun, Cheng Soon Ong, Soeren Sonnenburg # All rights reserved. # # Redistribution and use in source and binary forms, with or without # modification, are permitted provided that the following conditions are # met: # # * Redistributions of source code must retain the above copyright # notice, this list of conditions and the following disclaimer. # * Redistributions in binary form must reproduce the above # copyright notice, this list of conditions and the following disclaimer # in the documentation and/or other materials provided with the # distribution. # * Neither the names of the Technical University of Berlin, ETH # Zürich, or Fraunhofer FIRST nor the names of its contributors may be # used to endorse or promote products derived from this software without # specific prior written permission. # # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS # "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT # LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR # A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT # OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, # SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT # LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, # DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY # THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. class String # :nodoc: def truncate(maxlen) if length > maxlen self[0..maxlen-3] + "..." else self end end end module ARFF # A class for loading and saving ARFF-Files. # # Currently, handles the following attributes: # # * real, numeric, integer, string attributes. # # Date/relational attributes and sparse data is not supported yet. # # The first comment in a file is available via the +comment+ # attribute of the class. # # You can either load a file using ARFF.load or load the # data from a string using ARFF.string. class ARFFFile # The name of the data set. attr_accessor :relation # The initial comment in the file attr_accessor :comment # The names of the attributes (use define_attribute to set). attr_reader :attribute_names # The attribute types (hash) (use define_attribute to set). attr_reader :attribute_types # Additional data on the types (hash) (use define_attribute # to set). attr_reader :attribute_data # The actual data. attr_accessor :data # Create new ARFF File. def initialize @relation = '' @comment = [] @attribute_names = [] @attribute_types = Hash.new @attribute_data = Hash.new @data = [] @state = :comment end # Define an attribute by its name, type and potentially # further data. (For example, for ordinal types, the possible # values. def define_attribute(name, type, data=nil) @attribute_names << name @attribute_types[name] = type @attribute_data[name] = data if data end # Read the type of attribute +name+. def attribute_type(name) @attribute_types[name] end # Read the attribute data. #def attribute_data(name) # @attribute_data[name] #end # Load an ARFF file. def self.load(file) arff = nil open(file, 'r') {|f| arff = ARFFFile.parse(f.read) } return arff end # Construct an ARFFFile from a string. def self.parse(string) arff = ARFFFile.new arff.parse_file(string) return arff end # Load contents from a string. def parse_file(string) string.split("\n").each_with_index do |line, lineno| parse_line(line.chomp, lineno+1) end end ####### private ####### # Parse a single line. Uses a small state machine to keep track of # where we are. First comment is collected def parse_line(line, lineno) case @state when :comment if line =~ /^%/ @comment << line[2..-1] else @comment = @comment.join("\n") @state = :in_header parse_line(line, lineno) end when :in_header case line.downcase when /^@relation/i parse_relation_definition(line, lineno) when /^@attribute/i parse_attribute_definition(line, lineno) when /^@data/i @state = :data_section end when :data_section unless line =~ /^%/ or line.strip.size == 0 parse_data(line, lineno) end end end # Define an attribute as specified by line. def parse_attribute_definition(line, lineno) keyword, name, type = line.scan /[a-zA-Z_][a-zA-Z0-9_]*|\{[^\}]+\}|\'[^\']+\'|\"[^\"]+\"/ name = name[1...-1] if name[0] == ?' and name[-1] == ?' name = name[1...-1] if name[0] == ?" and name[-1] == ?" if type.downcase == 'real' or type.downcase == 'numeric' or type.downcase == 'integer' define_attribute(name, :numeric) elsif type.downcase == 'string' define_attribute(name, :string) elsif type =~ /\{([^\}]+)\}/ define_attribute(name, :nominal, $1.split(',').map {|s| s.strip}) else raise "Attributes of type \"#{type}\" not supported (yet)" end end # Define the name of the relation based on line. def parse_relation_definition(line, lineno) keyword, name = line.scan /[a-zA-Z_][a-zA-Z0-9_]*|\'[^\']+?\'|\"[^\"]+?\"/ #puts "Relation: #{name}" @relation = name end NUMERIC = /\A\s*[+-]?[0-9]+(?:\.[0-9]*(?:[eE]-?[0-9]+)?)?\s*\Z/ # Parse data line. def parse_data(line, lineno) if line[0] == ?{ and line[-1] == ?} raise "Sparse data not supported (yet)" else line = line.split(',').map{|s| s.strip} if line.size != @attribute_names.size puts "Warning: line #{lineno} does not contain the right number of elements (should be #{attribute_names.size}, got #{line.size})" return end datum = [] line.zip(@attribute_names).each do |e, a| case @attribute_types[a] when :numeric if e =~ NUMERIC datum << e.to_f else puts "Warning: line #{lineno} uses a non-numeric value \"#{e}\" for attribut \"#{a}\"." return end when :string datum << e when :nominal unless @attribute_data[a].include? e puts "Warning: line #{lineno} uses undefined nominal value \"#{e}\" for attribut \"#{a}\"." return end datum << e end end @data << datum end end ###### public ###### # generate a somewhat informative representation def dump s = [] s << "ARFF File representing relation \"#{@relation}\" with #{@data.length} data points" s << "" s << "Attributes:" for a in @attribute_names case @attribute_types[a] when :numeric s << " numeric attribute #{a}" when :string s << " string attribute #{a}" when :nominal s << " nominal attribute #{a} with values #{@attribute_data[a].join ', '}" end end s << "" s << "Comment starts with:" s << " > " + @comment[0..200].gsub(/\n/m, "\n > ") + "..." s << "" s << "First 5 data points:" for d in @data[0...5] s << d.map{|e| e.to_s}.join(', ').truncate(70) end s.join "\n" end # Write the arff file to a file. def save(file) open(file, "w") {|f| f.write(write)} end # Write the arfffile to a string. def write out = [] out << '% ' + comment.gsub(/\n/m, "\n% ") out << "@relation #{write_string(relation)}\n" for a in attribute_names case attribute_type(a) when :numeric out << "@attribute #{write_string(a)} numeric" when :string out << "@attribute #{write_string(a)} string" when :nominal out << "@attribute #{write_string(a)} {#{attribute_data[a].join(',')}}" end end out << "\n@data" for d in data line = [] d.zip(attribute_names).each do |e, a| case attribute_type(a) when :numeric line << e.to_s when :string line << write_string(e) when :nominal line << e end end out << line.join(',') end out.join("\n") + "\n" end ####### private ####### # write a string. encapsulate it in 's if it contains spaces def write_string(s) if s =~ /\s/ '\'' + s + '\'' else s end end end end ruby/arff_test.rb0000644000175200017530000000611611116205714013352 0ustar mikiomikio# Copyright (c) 2008, Mikio L. Braun, Cheng Soon Ong, Soeren Sonnenburg # All rights reserved. # # Redistribution and use in source and binary forms, with or without # modification, are permitted provided that the following conditions are # met: # # * Redistributions of source code must retain the above copyright # notice, this list of conditions and the following disclaimer. # * Redistributions in binary form must reproduce the above # copyright notice, this list of conditions and the following disclaimer # in the documentation and/or other materials provided with the # distribution. # * Neither the names of the Technical University of Berlin, ETH # Zürich, or Fraunhofer FIRST nor the names of its contributors may be # used to endorse or promote products derived from this software without # specific prior written permission. # # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS # "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT # LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR # A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT # OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, # SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT # LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, # DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY # THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. require 'test/unit' require 'arff' class ArffTest < Test::Unit::TestCase def parse(s) ARFF::ARFFFile.parse s end def test_comment a = parse '% first comment' assert_equal ['first comment'], a.comment end def test_relation a = parse '@relation test' assert_equal 'test', a.relation a = parse '@RELATION test' assert_equal 'test', a.relation end def test_real_attribute a = parse '@attribute foo real' assert_equal ['foo'], a.attribute_names assert_equal :numeric, a.attribute_types['foo'] assert_equal nil, a.attribute_data['foo'] a = parse '@attribute \'foo\' integer' assert_equal ['foo'], a.attribute_names assert_equal :numeric, a.attribute_types['foo'] assert_equal nil, a.attribute_data['foo'] end def test_nominal_attribute a = parse '@attribute foo { 1, 2, 3 }' assert_equal :nominal, a.attribute_types['foo'] assert_equal %w(1 2 3), a.attribute_data['foo'] end def test_data puts "This should emit two warnings on line 6 and 7!" a = parse <= 1 && l(1) == '%' if length(l) >= 2 if l(2) == ' ' l = l(2:end); end comment = horzcat(comment, l(2:end)); else comment = horzcat(comment, ''); end else state = 'header'; C.comment = comment; retry = 1; end case 'header' %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ll = lower(l); if startswith('@relation ', ll) W = split(l); C.relation = W{2}; elseif startswith('@attribute ', ll) W = split(l); name = W{2}; type = W{3}; lowertype = lower(type); switch lowertype case 'real' addattribute(name, 'numeric', []) case 'integer' addattribute(name, 'numeric', []) case 'numeric' addattribute(name, 'numeric', []) case 'string' addattribute(name, 'string', []) otherwise % paste type definition together in case there was % a space in there if type(1) == '{' if type(end) ~= '}' J = 3; while J <= length(W) && type(1) == '{' && type(end) ~= '}' J = J + 1; type = horzcat(type, W{J}); end if J > length(W); warning(['syntax error in nominal attribute definition: missing ' ... 'closing "}"']) break end end % check for nominal type definition if type(1) == '{' && type(end) == '}' values = type(2:end-1); values = splitby(values, ','); addattribute(W{2}, 'nominal', values); end else warning('cannot parse attribute definition') end end elseif startswith('@data', ll) state = 'data'; % set up data array na = length(C.attributes); data = cell(1,na); for I = 1:na % fill in empty values switch C.attribute_types{I} case 'numeric' data{I} = []; case 'string' data{I} = {}; case 'nominal' data{I} = {}; end end items = 0; end case 'data' %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% if ~isempty(l) && l(1) ~= '%' tokens = splitby(l, ','); if length(tokens) ~= na warning(sprintf('wrong number of values (expected %d, got %d)', ... na, length(tokens))); continue end items = items + 1; for I = 1:na value = tokens{I}; switch C.attribute_types{I} case 'numeric' value = str2num(value); if isempty(value) warning('cannot parse numeric value') continue end case 'string' % everythings okay case 'nominal' ad = C.attribute_data{I}; found = 0; for J = 1:length(ad) if strcmp(value, ad{J}) found = 1; end end if ~found warning('illegal nominal value') continue end end data{I} = vertcat(data{I}, value); end end end end ARFF = C; ARFF.data = data; ARFF.size = items; if warnings > 0 ARFF.warnings = warnings; end fclose(f); % check whether a string l starts with head function flag = startswith(head, l) if length(l) >= length(head) flag = strcmp(head, l(1:length(head))); else flag = 0; end end % Split a string by white-spaces function W = split(S) W = {}; while ~isempty(S) [T, S] = strtok(S); W = horzcat(W, T); end end % Split a string by a delimiter, remove whitespaces. function W = splitby(S, D) I = 1; W = {}; while ~isempty(S) J = strfind(S(2:end), D); if isempty(J) break end T = S(I:J); S = S(J+2:end); W = horzcat(W, trim(T)); end T = trim(S); if ~isempty(S) W = horzcat(W, T); end end % Remove whitespaces from front and back. function S = trim(S) while S(1) == ' ' S = S(2:end) end while S(end) == ' ' S = S(1:end-1) end end function addattribute(name, type, data) C.attributes = horzcat(C.attributes, name); C.attribute_types = horzcat(C.attribute_types, type); C.attribute_data = horzcat(C.attribute_data, { data }); end function warning(msg) fprintf('warning line %d: %s\n', lineno, msg); warnings = warnings + 1; end end % of arffload % Copyright (c) 2008, Mikio L. Braun, Cheng Soon Ong, Soeren Sonnenburg % All rights reserved. % % Redistribution and use in source and binary forms, with or without % modification, are permitted provided that the following conditions are % met: % % * Redistributions of source code must retain the above copyright % notice, this list of conditions and the following disclaimer. % * Redistributions in binary form must reproduce the above % copyright notice, this list of conditions and the following disclaimer % in the documentation and/or other materials provided with the % distribution. % * Neither the names of the Technical University of Berlin, ETH % Zürich, or Fraunhofer FIRST nor the names of its contributors may be % used to endorse or promote products derived from this software without % specific prior written permission. % % THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS % "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT % LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR % A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT % OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, % SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT % LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, % DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY % THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT % (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE % OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. matlab/arffsave.m0000644000175200017530000000755011116206061013301 0ustar mikiomikiofunction arffsave(ARFF, filename) % arffsave - save an arff structure to a file % % SYNPOSIS % success = arffsave(ARFF) % AUTHOR % Mikio L. Braun, mikio@cs.tu-berlin.de % see below for copyright information % do some checks on the structure to make sure we're actually % dealing with an ARFF structure... . ARFF_FIELDS = { 'attributes', 'attribute_types', ... 'attribute_data', 'data', 'relation', 'size' }; if ~isstruct(ARFF) || ~all(isfield(ARFF, ARFF_FIELDS)) error('You must pass a structure. See the documentation'); end na = length(ARFF.attributes); if length(ARFF.attribute_types) ~= na error('field attribute_types must have the same length as the field attributes') end if length(ARFF.attribute_data) ~= na error('field attribute_data must have the same length as the field attributes') end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % write initial comment f = fopen(filename, 'w'); if isfield(ARFF, 'comment') comment = ARFF.comment; for I = 1:length(comment) fprintf(f, '%% %s\n', comment{I}); end end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % write relation definition fprintf(f, '@relation %s\n', ARFF.relation); %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % write attribute definitions for I = 1:na fprintf(f, '@attribute %s ', ARFF.attributes{I}); switch ARFF.attribute_types{I} case 'numeric' fprintf(f, 'numeric'); case 'string' fprintf(f, 'string'); case 'nominal' ad = ARFF.attribute_data{I}; fprintf(f, '{%s', ad{1}); for J = 2:length(ad) fprintf(f, ',%s', ad{J}); end fprintf(f, '}'); otherwise error(sprintf('Unknown attribute type %s', ARFF.attribute_types{I})) end fprintf(f, '\n'); end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % write data fprintf(f, '@data\n'); for I = 1:ARFF.size print_datum(ARFF, 1, 1); for J = 2:na fprintf(f, ','); print_datum(ARFF, I, J); end fprintf(f, '\n'); end fclose(f); function print_datum(ARFF, I, J) values = ARFF.data{J}; switch ARFF.attribute_types{J} case 'numeric' fprintf(f, '%f', values(I)); case 'string' fprintf(f, '%s', values{I}); case 'nominal' fprintf(f, '%s', values{I}); end end end % Copyright (c) 2008, Mikio L. Braun, Cheng Soon Ong, Soeren Sonnenburg % All rights reserved. % % Redistribution and use in source and binary forms, with or without % modification, are permitted provided that the following conditions are % met: % % * Redistributions of source code must retain the above copyright % notice, this list of conditions and the following disclaimer. % * Redistributions in binary form must reproduce the above % copyright notice, this list of conditions and the following disclaimer % in the documentation and/or other materials provided with the % distribution. % * Neither the names of the Technical University of Berlin, ETH % Zürich, or Fraunhofer FIRST nor the names of its contributors may be % used to endorse or promote products derived from this software without % specific prior written permission. % % THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS % "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT % LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR % A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT % OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, % SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT % LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, % DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY % THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT % (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE % OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. java/dist/0000755000175200017530000000000011113751030011741 5ustar mikiomikiojava/dist/README.TXT0000644000175200017530000000265011116210153013301 0ustar mikiomikio======================== BUILD OUTPUT DESCRIPTION ======================== When you build an Java application project that has a main class, the IDE automatically copies all of the JAR files on the projects classpath to your projects dist/lib folder. The IDE also adds each of the JAR files to the Class-Path element in the application JAR files manifest file (MANIFEST.MF). To run the project from the command line, go to the dist folder and type the following: java -jar "Dataformat.jar" To distribute this project, zip up the dist folder (including the lib folder) and distribute the ZIP file. Notes: * If two JAR files on the project classpath have the same name, only the first JAR file is copied to the lib folder. * Only JAR files are copied to the lib folder. If the classpath contains other types of files or folders, none of the classpath elements are copied to the lib folder. In such a case, you need to copy the classpath elements to the lib folder manually after the build. * If a library on the projects classpath also has a Class-Path element specified in the manifest,the content of the Class-Path element has to be on the projects runtime path. * To set a main class in a standard Java project, right-click the project node in the Projects window and choose Properties. Then click Run and enter the class name in the Main Class field. Alternatively, you can manually type the class name in the manifest Main-Class element. java/dist/javadoc/0000755000175200017530000000000011113751673013365 5ustar mikiomikiojava/dist/javadoc/serialized-form.html0000644000175200017530000001312711116210153017335 0ustar mikiomikio Serialized Form
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ArffFile
ArffFileParseError
java/dist/javadoc/resources/0000755000175200017530000000000011113751031015363 5ustar mikiomikiojava/dist/javadoc/resources/inherit.gif0000644000175200017530000000007111113751031017512 0ustar mikiomikioGIF89a, DrjԐ;߀Q@N;java/dist/javadoc/edu/0000755000175200017530000000000011113751031014126 5ustar mikiomikiojava/dist/javadoc/edu/ida/0000755000175200017530000000000011113751031014663 5ustar mikiomikiojava/dist/javadoc/edu/ida/dataformat/0000755000175200017530000000000011113751673017021 5ustar mikiomikiojava/dist/javadoc/edu/ida/dataformat/package-use.html0000644000175200017530000001413611116210153022063 0ustar mikiomikio Uses of Package edu.ida.dataformat
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Uses of Package
edu.ida.dataformat

Classes in edu.ida.dataformat used by edu.ida.dataformat
ArffFile
          A class for reading and writing Arff-Files.
ArffFileParseError
          A parse error in an ArffFile.
 

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edu.ida.dataformat
Class ArffFileParseError

java.lang.Object
  extended by java.lang.Throwable
      extended by java.lang.Exception
          extended by edu.ida.dataformat.ArffFileParseError
All Implemented Interfaces:
java.io.Serializable
public class ArffFileParseError
extends java.lang.Exception

A parse error in an ArffFile. Constructs an error message including the line number.

See Also:
Serialized Form

Constructor Summary
ArffFileParseError(int lineno, java.lang.String string)
          Construct a new ArffFileParseErrro object.
 
Method Summary
 
Methods inherited from class java.lang.Throwable
fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

ArffFileParseError

public ArffFileParseError(int lineno,
                          java.lang.String string)
Construct a new ArffFileParseErrro object.

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Hierarchy For Package edu.ida.dataformat

Class Hierarchy

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Classes 
ArffFile
Exceptions 
ArffFileParseError
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Package edu.ida.dataformat

A Package for reading and writing ARFF Files.

See:
          Description

Class Summary
ArffFile A class for reading and writing Arff-Files.
 

Exception Summary
ArffFileParseError A parse error in an ArffFile.
 

Package edu.ida.dataformat Description

A Package for reading and writing ARFF Files. ARFF Files were developed in the Weka project. For more information, see here.

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edu.ida.dataformat
Class ArffFile

java.lang.Object
  extended by edu.ida.dataformat.ArffFile

public class ArffFile
extends java.lang.Object

A class for reading and writing Arff-Files.

You can either load a file, parse a string or a BufferedReader. Afterwards, you can extract the information with the methods getComment(), getNumberOfAttributes(), getAttributeName(), getAttributeType(), getAttributeData().

Alternative, you can construct an empty ArffFile object, and then use setComment(), defineAttribute(), add() to fill in the data and then save to a file with save(), or to a string with write().

The first comment in an ArffFile is extracted and made available through the *Comment() accessors. Usually, this comment contains some interesting information about the data set.

Currently, the class only supports numerical, string and nominal attributes. It also does not support sparse storage (yet).

Constructor Summary
ArffFile()
          Construct an empty ArffFile.
 
Method Summary
 void add(java.lang.Object[] datum)
          Add a datum.
 void defineAttribute(java.lang.String name, java.lang.String type, java.lang.String[] data)
          Define a new attribute.
 java.lang.String dump()
          Generate a string which describes the data set.
 java.lang.String[] getAttributeData(java.lang.String name)
          Get additional information on the attribute.
 java.lang.String getAttributeName(int idx)
          Get the name of an attribute.
 java.lang.String getAttributeType(java.lang.String name)
          Get the type of an attribute.
 java.lang.String getComment()
          Get the initial comment of the relation.
 int getDataSize()
           
 java.lang.Object[] getDatum(int i)
           
 int getNumberOfAttributes()
          Get the number of attributes.
 java.lang.String getRelation()
          Get the name of the relation.
static ArffFile load(java.lang.String filename)
          Load an ArffFile.
static void main(java.lang.String[] args)
          Main function for debugging.
 void parse(java.io.BufferedReader r)
          Parse an ArffFile from a BufferedReader.
static ArffFile parse(java.lang.String l)
          Parse an ArffFile from a string.
 void save(java.lang.String filename)
          Save the data into a file.
 void setComment(java.lang.String comment)
          Set the initial comment of the relation.
 void setRelation(java.lang.String relation)
          Set the name of the relation.
 java.lang.String write()
          Write the ArffFile to a string.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ArffFile

public ArffFile()
Construct an empty ArffFile.

Method Detail

load

public static ArffFile load(java.lang.String filename)
                     throws java.io.FileNotFoundException,
                            java.io.IOException,
                            ArffFileParseError
Load an ArffFile.

Throws:
java.io.FileNotFoundException
java.io.IOException
ArffFileParseError

parse

public static ArffFile parse(java.lang.String l)
                      throws java.io.IOException,
                             ArffFileParseError
Parse an ArffFile from a string.

Throws:
java.io.IOException
ArffFileParseError

parse

public void parse(java.io.BufferedReader r)
           throws java.io.IOException
Parse an ArffFile from a BufferedReader.

Throws:
java.io.IOException

defineAttribute

public void defineAttribute(java.lang.String name,
                            java.lang.String type,
                            java.lang.String[] data)
Define a new attribute. Type must be one of "numeric", "string", and "nominal". For nominal attributes, the allowed values must also be given. This variant of defineAttribute allows to set this data.

dump

public java.lang.String dump()
Generate a string which describes the data set.

write

public java.lang.String write()
Write the ArffFile to a string.

save

public void save(java.lang.String filename)
          throws java.io.IOException
Save the data into a file.

Throws:
java.io.IOException

main

public static void main(java.lang.String[] args)
Main function for debugging. Loads files from the argument list and dumps their contents to the System.out.

getRelation

public java.lang.String getRelation()
Get the name of the relation.

setRelation

public void setRelation(java.lang.String relation)
Set the name of the relation.

getComment

public java.lang.String getComment()
Get the initial comment of the relation.

setComment

public void setComment(java.lang.String comment)
Set the initial comment of the relation.

getNumberOfAttributes

public int getNumberOfAttributes()
Get the number of attributes.

getAttributeName

public java.lang.String getAttributeName(int idx)
Get the name of an attribute.

getAttributeType

public java.lang.String getAttributeType(java.lang.String name)
Get the type of an attribute. Currently, the attribute types are "numeric", "string", and "nominal". For nominal attributes, use getAttributeData() to retrieve the possible values for the attribute.

getAttributeData

public java.lang.String[] getAttributeData(java.lang.String name)
Get additional information on the attribute. This data is used for nominal attributes to define the possible values.

add

public void add(java.lang.Object[] datum)
Add a datum. No checking of the data types is performed!

getDataSize

public int getDataSize()

getDatum

public java.lang.Object[] getDatum(int i)
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edu.ida.dataformat.ArffFileParseError

Uses of ArffFileParseError in edu.ida.dataformat
 

Methods in edu.ida.dataformat that throw ArffFileParseError
static ArffFile ArffFile.load(java.lang.String filename)
          Load an ArffFile.
static ArffFile ArffFile.parse(java.lang.String l)
          Parse an ArffFile from a string.
 

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edu.ida.dataformat.ArffFile

Uses of ArffFile in edu.ida.dataformat
 

Methods in edu.ida.dataformat that return ArffFile
static ArffFile ArffFile.load(java.lang.String filename)
          Load an ArffFile.
static ArffFile ArffFile.parse(java.lang.String l)
          Parse an ArffFile from a string.
 

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Constant Field Values

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java/dist/javadoc/index-files/0000755000175200017530000000000011113751031015560 5ustar mikiomikiojava/dist/javadoc/index-files/index-2.html0000644000175200017530000001414511116210153017717 0ustar mikiomikio D-Index
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D

defineAttribute(String, String, String[]) - Method in class edu.ida.dataformat.ArffFile
Define a new attribute.
dump() - Method in class edu.ida.dataformat.ArffFile
Generate a string which describes the data set.
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W

write() - Method in class edu.ida.dataformat.ArffFile
Write the ArffFile to a string.
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P

parse(String) - Static method in class edu.ida.dataformat.ArffFile
Parse an ArffFile from a string.
parse(BufferedReader) - Method in class edu.ida.dataformat.ArffFile
Parse an ArffFile from a BufferedReader.
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save(String) - Method in class edu.ida.dataformat.ArffFile
Save the data into a file.
setComment(String) - Method in class edu.ida.dataformat.ArffFile
Set the initial comment of the relation.
setRelation(String) - Method in class edu.ida.dataformat.ArffFile
Set the name of the relation.
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A

add(Object[]) - Method in class edu.ida.dataformat.ArffFile
Add a datum.
ArffFile - Class in edu.ida.dataformat
A class for reading and writing Arff-Files.
ArffFile() - Constructor for class edu.ida.dataformat.ArffFile
Construct an empty ArffFile.
ArffFileParseError - Exception in edu.ida.dataformat
A parse error in an ArffFile.
ArffFileParseError(int, String) - Constructor for exception edu.ida.dataformat.ArffFileParseError
Construct a new ArffFileParseErrro object.
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edu.ida.dataformat - package edu.ida.dataformat
A Package for reading and writing ARFF Files.
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G

getAttributeData(String) - Method in class edu.ida.dataformat.ArffFile
Get additional information on the attribute.
getAttributeName(int) - Method in class edu.ida.dataformat.ArffFile
Get the name of an attribute.
getAttributeType(String) - Method in class edu.ida.dataformat.ArffFile
Get the type of an attribute.
getComment() - Method in class edu.ida.dataformat.ArffFile
Get the initial comment of the relation.
getDataSize() - Method in class edu.ida.dataformat.ArffFile
 
getDatum(int) - Method in class edu.ida.dataformat.ArffFile
 
getNumberOfAttributes() - Method in class edu.ida.dataformat.ArffFile
Get the number of attributes.
getRelation() - Method in class edu.ida.dataformat.ArffFile
Get the name of the relation.
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load(String) - Static method in class edu.ida.dataformat.ArffFile
Load an ArffFile.
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M

main(String[]) - Static method in class edu.ida.dataformat.ArffFile
Main function for debugging.
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ArffFile
ArffFileParseError
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How This API Document Is Organized

This API (Application Programming Interface) document has pages corresponding to the items in the navigation bar, described as follows.

Package

Each package has a page that contains a list of its classes and interfaces, with a summary for each. This page can contain four categories:

Class/Interface

Each class, interface, nested class and nested interface has its own separate page. Each of these pages has three sections consisting of a class/interface description, summary tables, and detailed member descriptions:

Each summary entry contains the first sentence from the detailed description for that item. The summary entries are alphabetical, while the detailed descriptions are in the order they appear in the source code. This preserves the logical groupings established by the programmer.

Annotation Type

Each annotation type has its own separate page with the following sections:

Enum

Each enum has its own separate page with the following sections:

Use

Each documented package, class and interface has its own Use page. This page describes what packages, classes, methods, constructors and fields use any part of the given class or package. Given a class or interface A, its Use page includes subclasses of A, fields declared as A, methods that return A, and methods and constructors with parameters of type A. You can access this page by first going to the package, class or interface, then clicking on the "Use" link in the navigation bar.

Tree (Class Hierarchy)

There is a Class Hierarchy page for all packages, plus a hierarchy for each package. Each hierarchy page contains a list of classes and a list of interfaces. The classes are organized by inheritance structure starting with java.lang.Object. The interfaces do not inherit from java.lang.Object.

Deprecated API

The Deprecated API page lists all of the API that have been deprecated. A deprecated API is not recommended for use, generally due to improvements, and a replacement API is usually given. Deprecated APIs may be removed in future implementations.

Index

The Index contains an alphabetic list of all classes, interfaces, constructors, methods, and fields.

Prev/Next

These links take you to the next or previous class, interface, package, or related page.

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These links show and hide the HTML frames. All pages are available with or without frames.

Serialized Form

Each serializable or externalizable class has a description of its serialization fields and methods. This information is of interest to re-implementors, not to developers using the API. While there is no link in the navigation bar, you can get to this information by going to any serialized class and clicking "Serialized Form" in the "See also" section of the class description.

Constant Field Values

The Constant Field Values page lists the static final fields and their values.

This help file applies to API documentation generated using the standard doclet.

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Braun, Cheng Soon Ong, Soeren Sonnenburg All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the names of the Technical University of Berlin, ETH Zürich, or Fraunhofer FIRST nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. README0000644000175200017530000000157611116201040010740 0ustar mikiomikiodataformat 0.1 - a collection of modules for reading and writing machine learning data sets The goal of this project is to provide code for reading and writing machine learning data sets for as many programming languages as possible. Using these code, it should become much easier to have code written in different languages speak to each other. Currently, we are focusing on the ARFF file format (http://weka.sourceforge.net/wekadoc/index.php/en:ARFF_%283.5.6%29), developed in the Weka project (http://www.cs.waikato.ac.nz/~ml/). Currently covered languages are: - python - ruby - matlab - java C and C++ are next on the list. ARFF is covered except for: - sparse features - date attributes - relational attributes - missing values - instance weights Some things might not work as expected, in particular - strings with commas in them But we're working on that.