delphin 0.0.1

data/README

@@ -0,0 +1,17 @@
+= Ruby Utilities for DELPH-IN
+
+This is a set of Ruby utilities for the {Delphin}[http://www.delph-in.net/] HPSG processing project.
+
+= History
+
+1.0.0:: Profile data structures
+
+= Copyright
+
+Copyright 2009, William Patrick McNeill
+
+This program is distributed under the GNU General Public License.
+
+= Author
+
+W.P. McNeill mailto:billmcn@gmail.com

data/bin/cleanup-profile

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+#!/usr/bin/env ruby
+
+require "delphin"
+require "fileutils"
+require "optparse"
+
+
+# Display an error message and the generic help message and exit.
+def error_exit(parser, error, exit_code = -1)
+  puts error
+  puts parser.help
+  exit(exit_code)
+end
+
+
+delete = false
+
+parser = OptionParser.new do |opts|
+  opts.banner =<<-EOTEXT
+#{File.basename(__FILE__)} [OPTION] glob [table table...]
+
+List all invalid TSDB profiles matching the specified file glob and optionally delete them.
+
+A directory is a valid profile if it contains a non-empty relations file.  Other required non-empty table files may be specified as command line arguments.
+
+By default this script merely prints the names of invalid profiles.  It will also delete them if the delete switch is specified.
+
+Bracket characters in globs must be escaped with two backslashes, e.g. \\\\[
+EOTEXT
+  opts.on("-l", "--logging LEVEL", "Logging level") do |level|
+    Delphin.set_log_level(eval("Logger::#{level.upcase}"))
+  end
+
+  opts.on("-d", "--delete", "Delete invalid profiles") do
+    delete = true
+  end
+end
+
+begin
+  parser.parse!
+rescue OptionParser::ParseError => e
+  error_exit(parser, e)
+end
+
+if ARGV.length < 1
+  error_exit(parser, "Incorrect number of arguments.")
+end
+
+glob = ARGV.shift
+table_names = ARGV
+
+Pathname.glob(glob).select {|d| d.directory?}.collect do |d|
+  Delphin::LOGGER.debug("Profile directory #{d}")
+  begin
+    profile = Delphin::Profile.new(d)
+    table_names.each do |table_name|
+      table = profile[table_name]
+      if File.zero?(table.filename)
+        raise Delphin::EmptyDataFile.new(table_name, profile)
+      end
+    end
+  rescue Delphin::InvalidProfileException => e
+    puts e.message
+    FileUtils.rm_rf(d) if delete
+    next
+  end
+end

data/bin/score-profile

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+#!/usr/bin/env ruby
+
+require "delphin"
+require "optparse"
+require "yaml"
+
+
+# Display an error message and the generic help message and exit.
+def error_exit(parser, error, exit_code = -1)
+  puts error
+  puts parser.help
+  exit(exit_code)  
+end
+
+
+full_name = false
+to_yaml = false
+
+parser = OptionParser.new do |opts|
+  opts.banner =<<-EOTEXT
+#{File.basename(__FILE__)} [OPTION] glob
+
+Print a summary of the scores in all the profiles matching the specified file
+glob.
+
+Bracket characters in paths must be escaped with two backslashes, e.g. \\\\[
+EOTEXT
+  opts.on("-l", "--logging LEVEL", "Logging level") do |level|
+    Delphin.set_log_level(eval("Logger::#{level.upcase}"))
+  end
+
+  opts.on("-f", "--full-name", "Print full directory name") do
+    full_name = true
+  end
+
+  opts.on("-y", "--yaml", "Output results as YAML") do
+    to_yaml = true
+  end
+
+end
+
+begin
+  parser.parse!
+rescue OptionParser::ParseError => e
+  error_exit(parser, e)
+end
+
+if not ARGV.length == 1
+  error_exit(parser, "Incorrect number of arguments.")
+end
+
+stats = Delphin.summarize_folds(File.expand_path(ARGV.first))
+s = if to_yaml
+  YAML::dump(stats)
+else
+  stats.collect do |stat|
+    stat[3] = File.basename(stat[3]) if not full_name
+    stat.join(" ")
+  end.join("\n")
+end
+puts s

data/lib/delphin.rb

@@ -0,0 +1,377 @@
+# Copyright 2009 William Patrick McNeill
+#
+# This file is part of DELPHN-IN Ruby Utility Package.
+#
+# The DELPHN-IN Ruby Utility Package is free software; you can redistribute it
+# and/or modify it under the terms of the GNU General Public License as
+# published by the Free Software Foundation; either version 2 of the License,
+# or (at your option) any later version.
+#
+# The DELPHN-IN Ruby Utility Package is distributed in the hope that it will
+# be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
+# Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along with
+# editalign; if not, write to the Free Software Foundation, Inc., 51 Franklin
+# St, Fifth Floor, Boston, MA 02110-1301 USA
+
+require "logger"
+require "pathname"
+require "set"
+
+# Utilities for use with the DELPH-IN project.
+module Delphin
+  VERSION = "0.0.1"
+
+  # Create the logger and set its default log level to ERROR.  This function
+  # is called when the module is loaded.
+  def Delphin.initialize_logger
+    logger = Logger.new(STDERR)
+    logger.level = Logger::ERROR
+    logger.datetime_format = "%Y-%m-%d %H:%M:%S"
+    logger
+  end
+
+  private_class_method :initialize_logger
+
+  # Logger used by all objects in this module.  This is initialized at module
+  # load time.  The default log level is ERROR.
+  LOGGER = initialize_logger
+
+  # Set the logging level.  For example:
+  #
+  #   > Delphin.set_log_level(Logger::DEBUG)
+  def Delphin.set_log_level(level)
+    Delphin::LOGGER.level = level
+  end
+
+  # Abstract base class for all exceptions raised by this module.
+  class InvalidProfileException < Exception
+  end
+
+  class MissingDataFile < InvalidProfileException
+    def initialize(name, profile)
+      @name = name
+      @profile = profile
+    end
+
+    def to_s
+      "Missing data file for table #{@name} in #{@profile}."
+    end
+  end
+
+  class EmptyDataFile < InvalidProfileException
+    def initialize(name, profile)
+      @name = name
+      @profile = profile
+    end
+
+    def to_s
+      "Empty data file for table #{@name} in #{@profile}."
+    end
+  end
+
+  class MissingRelationsFile < InvalidProfileException
+    def initialize(directory)
+      @directory = directory
+    end
+    
+    def to_s
+      "Missing relations file in #{@directory}."
+    end
+  end
+
+  class InvalidRelationsFile < InvalidProfileException
+    def initialize(filename, linenum, line)
+      @filename = filename
+      @linenum = linenum
+      @line = line
+    end
+
+    def to_s
+      "Invalid line #{@linenum} #{@filename}\n#{@line}"
+    end
+  end
+
+  # Given a file glob that picks out profiles, extract the specified numerical
+  # information, calculate statistics, and return a table sorted by mean.
+  #
+  # [_glob_] A file glob
+  def Delphin.summarize_folds(glob)
+    Pathname.glob(glob).select {|d| d.directory?}.collect do |d|
+      LOGGER.debug("Profile directory #{d}")
+      begin
+        s = Profile.new(d).statistics("fold", "f-accuracy")
+      rescue InvalidProfileException => e
+        LOGGER.error(e.message)
+        next
+      end
+      [s.mean, s.sdev, s.range, d.to_s]
+    # Filter out nils left in the list by handled exceptions.
+    end.select{|r| not r.nil?}.sort_by {|r| -r.first}
+  end
+
+
+  # The name of a Logon TSDB output profile.
+  #
+  # These are long strings with information about the features used to
+  # generate them in brackets.
+  class OutputProfileName < Struct.new(:prefix, :grandparenting,
+                                       :constituent_weight, :active_edges,
+                                       :ngram_size, :ngram_back_off,
+                                       :relative_tolerance, :variance)
+    # The basename of the profile
+    attr_reader :name
+    
+    # Create a output profile name from a directory name
+    #
+    # Path information will be stripped from the name parameter.
+    #
+    # [_name_] A directory name    
+    def initialize(name)
+      @name = File.basename(name)
+      @name =~ /\[(\S+)\]\s     # 1 Prefix
+                GP\[(\d+)\]\s   # 2 Grandparenting
+                [+-]PT\s
+                [+-]LEX\s
+                CW\[(\d*)\]\s   # 3 Constituent weight
+                ([+-])AE\s      # 4 Active edges
+                NS\[(\d+)\]\s   # 5 N-gram size
+                NT\[\w*\]\s
+                ([+-])NB\s      # 6 N-gram backoff
+                LM\[\d+\]\s
+                FT\[:::\d+\]\s  
+                RS\[\]\s
+                MM\[\S+\]\s
+                MI\[\d+\]\s
+                RT\[(\d+(?:\.\d+)?e[+-]\d+)\]\s # 7 Relative tolerance
+                AT\[\d+(?:\.\d+)?e[+-]\d+\]\s
+                VA\[(\d+(?:\.\d+)?e[+-]\d+)?\]\s # 8 Variance
+                PC\[\d+\]
+               /x or
+        raise ArgumentError.new("Invalid profile name #{name}")
+      super($1, $2.to_i, $3.to_i, $4 == "+", $5.to_i, $6 == "+", $7.to_f,
+            $8.nil? ? nil : $8.to_f)
+    end
+    
+    def to_s
+      "#{prefix}:#{feature_string}"
+    end
+    
+    # Do this profile name and other have the all same machine learning
+    # features?
+    def equal_learner_features?(other)
+      [:grandparenting, :constituent_weight, :active_edges, :ngram_size,
+       :ngram_back_off, :relative_tolerance, :variance].all? do |feature|
+        send(feature) == other.send(feature)
+      end
+    end
+    
+    # A compact and readable representation of all the feature values.
+    def feature_string
+      [:grandparenting, :constituent_weight, :active_edges, :ngram_size,
+       :ngram_back_off, :relative_tolerance, :variance].collect do |feature|
+        "#{feature.to_s}=#{send(feature)}"
+      end.join(",")
+    end
+    
+  end # OutputProfileName
+
+
+  # A TSDB profile
+  class Profile
+    attr_reader :directory, :relations
+
+    def initialize(directory)
+      @directory = directory
+      begin
+        @relations = open(File.join(directory, "relations")) do |file|
+          RelationsFile.new(file)
+        end
+      rescue Errno::ENOENT
+        raise MissingRelationsFile.new(directory)
+      end
+    end
+
+    def inspect
+      "#{self.class}(#{directory})"
+    end
+
+    def to_s
+      inspect
+    end
+
+    # A list of all the tables in the profile
+    def tables
+      @relations.keys
+    end
+
+    # Open the specified table file.
+    def [](name)
+      ProfileTable.new(self, name, @relations[name])
+    end
+
+    # Retun mean and standard deviation for numeric values in the specified
+    # field.
+    def statistics(table, field)
+      s = self[table].collect {|r| r[field].to_f}
+      n = s.length
+      raise EmptyDataFile.new(table, self) if n.zero?
+      mean = (s.inject(0) {|sum, x| sum + x})/n
+      n = n-1 if n > 1
+      sdev = Math.sqrt((s.inject(0) {|sum, x| sum + (x-mean)**2})/n)
+      range = s.max - s.min
+      Struct.new(:mean, :sdev, :range).new(mean, sdev, range)
+    end
+  end
+
+
+  # A data table in a TSDB profile.
+  class ProfileTable
+    include Enumerable
+
+    attr_reader :profile, :name, :schema, :filename
+
+    def initialize(profile, name, schema)
+      @profile = profile
+      @name = name
+      @schema = schema
+      # Find the table containing this table.  It may be gzipped.      
+      filename = File.join(profile.directory, name)
+      gzname = filename + ".gz"
+      if File.exist?(filename)
+        @filename = filename
+        @file = open(filename)
+      elsif File.exist?(gzname)
+        @filename = gzname
+        @file = Zlib::GzipReader.open(gzname)
+      else
+        raise MissingDataFile.new(@name, @profile)
+      end
+    end
+
+    def inspect
+      "#{self.class}(#{name}) in #{profile}"
+    end
+
+    def to_s
+      inspect
+    end
+
+    # Enumerate the records in this table.
+    def each
+      @file.each do |line|
+        yield @schema.record(line.strip!)
+      end
+    end
+  end # ProfileTable
+
+
+  # A database schema table in a profile.
+  #
+  # This is a list of field labels and their types.
+  class ProfileTableSchema < Array
+    attr_reader :name, :keys, :partials
+
+    def initialize(init_name)
+      super()
+      @name = init_name
+      @keys = Set.new
+      @partials = Set.new
+    end
+
+    # The string representation is identical to what appears in the relations
+    # file.
+    def to_s
+      "#{name}:\n" + collect do |field|
+        s = "  #{field.label} :#{field.type}"
+        s += " :key" if is_key?(field.label)
+        s += " :partial" if is_partial?(field.label)
+        s
+      end.join("\n")
+    end
+
+    # Generate a data record from a line of text.
+    #
+    # A data record is a hash of field labels to values.
+    def record(text)
+      data_fields = text.split(/@/)
+      field_names = collect {|f| f.label}
+      field_types = collect {|f| f.type}
+      # Do type conversion if the field is of type integer.
+      data_fields = field_types.zip(data_fields).collect do |type, data|
+        case type
+        when :integer
+          data.to_i
+        else
+          data
+        end
+      end
+      Hash[*field_names.zip(data_fields).flatten]
+    end
+
+    # Add a new field and type.
+    def add_field(label, type, key = false, partial = false)
+      self.push(Struct.new(:label, :type).new(label, type))
+      @keys.add(label) if key
+      @partials.add(label) if partial
+    end
+
+    # Is the specified label a key?
+    def is_key?(label)
+      @keys.member?(label)
+    end
+
+    # Is the specified label a partial?
+    def is_partial?(label)
+      @partials.member?(label)
+    end
+  end # ProfileTableSchema
+
+
+  # A file that contains a set of database schema tables.
+  #
+  # This object is a hash of ProfileTableSchema objects indexed by table name.
+  class RelationsFile < Hash
+    def initialize(file)
+      super()
+      state = :outside_table
+      table_name = nil
+      file.each_with_index do |line,i|
+        # Remove comments and surrounding whitespace.
+        line.sub!(/#.*/, "")
+        line.strip!
+        case state
+        when :inside_table
+          if line.empty?
+            state = :outside_table
+          elsif line =~ /^(\S+)\s+:(\w+)(\s+:key)?(\s+:partial)?$/
+            # E.g. parse-id :integer :key
+            field, type = line.split
+            self[table_name].add_field($1, $2, !$3.nil?, !$4.nil?)
+          else
+            raise InvalidRelationsFile.new(filename, i+1, line)
+          end
+        when :outside_table
+          next if line.empty?
+          if line =~ /(\S+):/
+            # E.g. item:
+            table_name = $1
+            self[table_name] = ProfileTableSchema.new(table_name)
+            state = :inside_table
+          else
+            raise InvalidRelationsFile.new(filename, i+1, line)
+          end
+        end
+      end # each_with_index
+    end # initialize
+
+    # Print out a relations file
+    def to_s
+      values.map {|t| t.to_s}.join("\n\n")
+    end # to_s
+  end # RelationsFile
+
+
+end # Delphin

data/test/test_delphin.rb

@@ -0,0 +1,77 @@
+#!/usr/bin/env ruby
+
+#--
+
+# Copyright 2009 William Patrick McNeill
+#
+# This file is part of DELPN-IN Ruby Utility Package.
+#
+# The DELPN-IN Ruby Utility Package is free software; you can redistribute it
+# and/or modify it under the terms of the GNU General Public License as
+# published by the Free Software Foundation; either version 2 of the License,
+# or (at your option) any later version.
+#
+# The DELPN-IN Ruby Utility Package is distributed in the hope that it will be
+# useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
+# Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along with
+# editalign; if not, write to the Free Software Foundation, Inc., 51 Franklin
+# St, Fifth Floor, Boston, MA 02110-1301 USA
+#
+#++
+
+# Test cases for the Delphin module
+
+require "test/unit"
+require "delphin"
+
+
+class Schema < Test::Unit::TestCase
+  def test_stub
+    Delphin::ProfileTableSchema.new("schema")
+  end
+end
+
+class TestOutputProfileName < Test::Unit::TestCase
+  def setup
+    @name1 = "[tanaka-train] GP[0] +PT -LEX CW[1] +AE NS[4] NT[type] +NB LM[0] FT[:::1] RS[] MM[tao_lmvm] MI[5000] RT[1.0e-8] AT[1.0e-20] VA[1.0e+0] PC[100]"
+    @profile1 = Delphin::OutputProfileName.new(@name1)
+    @name2 = "[jhpstg] GP[0] +PT -LEX CW[] -AE NS[3] NT[type] +NB LM[0] FT[:::1] RS[] MM[tao_lmvm] MI[5000] RT[1.0e-6] AT[1.0e-20] VA[1.0e-4] PC[100]"
+    @profile2 = Delphin::OutputProfileName.new(@name2)    
+  end
+  
+  def test_valid_name
+    assert_equal(@name1, @profile1.name)
+    assert_equal("tanaka-train", @profile1.prefix)
+    assert_equal(0, @profile1.grandparenting)
+    assert_equal(1, @profile1.constituent_weight)
+    assert_equal(true, @profile1.active_edges)
+    assert_equal(4, @profile1.ngram_size)
+    assert_equal(true, @profile1.ngram_back_off)
+    assert_equal(1e-8, @profile1.relative_tolerance)
+    assert_equal(1, @profile1.variance)
+  end
+
+  def test_empty_variance
+    name = "[jhpstg] GP[0] +PT -LEX CW[2] +AE NS[2] NT[type] +NB LM[0] FT[:::1] RS[] MM[tao_lmvm] MI[5000] RT[1.0e-6] AT[1.0e-20] VA[] PC[100]"
+    profile = Delphin::OutputProfileName.new(name)
+    assert_equal(nil, profile.variance)
+  end
+
+  def test_feature_string
+    expected = "grandparenting=0,constituent_weight=1,active_edges=true,ngram_size=4,ngram_back_off=true,relative_tolerance=1.0e-08,variance=1.0"
+    assert_equal(expected, @profile1.feature_string)
+  end
+
+  def test_feature_equivalence
+    assert(@profile1.equal_learner_features?(@profile1))
+    assert((not @profile1.equal_learner_features?(@profile2)))
+  end
+  
+  def test_invalid_name
+    assert_raise(ArgumentError) { Delphin::OutputProfileName.new("bogus") }
+  end
+  
+end

metadata

@@ -0,0 +1,66 @@
+--- !ruby/object:Gem::Specification 
+name: delphin
+version: !ruby/object:Gem::Version 
+  version: 0.0.1
+platform: ruby
+authors: 
+- W.P. McNeill
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2009-09-23 00:00:00 -07:00
+default_executable: 
+dependencies: []
+
+description: |
+  This module is a Ruby wrapper for the DELPH-IN project.
+
+email: billmcn@gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- README
+files: 
+- test/test_delphin.rb
+- lib/delphin.rb
+- bin/cleanup-profile
+- bin/score-profile
+- README
+has_rdoc: true
+homepage: http://delphin.rubyforge.org/
+licenses: []
+
+post_install_message: 
+rdoc_options: 
+- - --title
+  - Delphin -- DELPH-IN utilities
+  - --main
+  - README
+  - --line-numbers
+  - --inline-source
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+requirements: []
+
+rubyforge_project: delphin
+rubygems_version: 1.3.5
+signing_key: 
+specification_version: 3
+summary: Ruby utilities for the DELPH-IN project
+test_files: 
+- test/test_delphin.rb