rcpm 0.1.0

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 967d41e31aae19de32a51334c9791c7eaded9773
+  data.tar.gz: aac5b07ef54940bfbbf7cf4ad233e1c942532311
+SHA512:
+  metadata.gz: 57699c6a3d6c2b2a91efb9ff404942edc60fabe87982b4aa58248469c38e96cc92a9366b5f0183bcc7ea163365cc03d666efc01175d673c7530897b51f5cd84b
+  data.tar.gz: f87f44a34a11a2eb2c22eb77997ec42feb07ac2488810cd683fc422d57d758e52c423ea2a670950d7100838b43694c2913f717611af1fa6cef7012f61789cbb0

data/.gitignore

@@ -0,0 +1,9 @@
+/.bundle/
+/.yardoc
+/Gemfile.lock
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/

data/CODE_OF_CONDUCT.md

@@ -0,0 +1,30 @@
+# Contributor Code of Conduct
+
+As contributors and maintainers of this project, we pledge to respect
+all people who contribute through reporting issues, posting feature
+requests, updating documentation, submitting pull requests or patches,
+and other activities.
+
+We are committed to making participation in this project a
+harassment-free experience for everyone, regardless of level of
+experience, gender, gender identity and expression, sexual orientation,
+disability, personal appearance, body size, race, age, or religion.
+
+Examples of unacceptable behavior by participants include the use of
+sexual language or imagery, derogatory comments or personal attacks,
+trolling, public or private harassment, insults, or other unprofessional
+conduct.
+
+Project maintainers have the right and responsibility to remove, edit,
+or reject comments, commits, code, wiki edits, issues, and other
+contributions that are not aligned to this Code of Conduct. Project
+maintainers who do not follow the Code of Conduct may be removed from
+the project team.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may
+be reported by opening an issue or contacting one or more of the project
+maintainers.
+
+This Code of Conduct is adapted from the [Contributor
+Covenant](http:contributor-covenant.org), version 1.0.0, available at
+[http://contributor-covenant.org/version/1/0/0/](http://contributor-covenant.org/version/1/0/0/)

data/Gemfile

@@ -0,0 +1,3 @@
+source 'https://rubygems.org'
+
+gemspec

data/LICENSE.txt

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2015 Michel Boaventura
+
+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.

data/README.md

@@ -0,0 +1,39 @@
+# Rcpm
+
+Welcome to your new gem! In this directory, you'll find the files you need to be able to package up your Ruby library into a gem. Put your Ruby code in the file `lib/rcpm`. To experiment with that code, run `bin/console` for an interactive prompt.
+
+TODO: Delete this and the text above, and describe your gem
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'rcpm'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install rcpm
+
+## Usage
+
+TODO: Write usage instructions here
+
+## Development
+
+After checking out the repo, run `bin/setup` to install dependencies. Then, run `bin/console` for an interactive prompt that will allow you to experiment. 
+
+To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release` to create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
+
+## Contributing
+
+1. Fork it ( https://github.com/[my-github-username]/rcpm/fork )
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create a new Pull Request

data/Rakefile

@@ -0,0 +1,9 @@
+require "bundler/gem_tasks"
+require 'rake/extensiontask'
+
+Rake::ExtensionTask.new('bk')
+
+RSpec::Core::RakeTask.new
+
+task :default => [:compile]
+task :test => [:compile]

data/bin/console

@@ -0,0 +1,14 @@
+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "rcpm"
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require "irb"
+IRB.start

data/bin/rcpm

@@ -0,0 +1,61 @@
+#!/bin/env ruby
+
+require 'bundler/setup'
+require 'rcpm'
+require 'csv'
+require 'set'
+require 'optparse'
+
+options = { k: 0, file: "" }
+
+optparse = OptionParser.new do |opts|
+  opts.banner = "Usage: rcpm -k K -f file1"
+
+  opts.on("-k K", Integer, "K value" ) do |k|
+    options[:k] = k
+  end
+
+  opts.on( "-f FILE", String, "File input" ) do |file|
+    options[:file] = file
+  end
+end
+
+begin
+  optparse.parse!
+rescue OptionParser::MissingArgument
+  puts optparse
+  exit
+end
+
+if options[:k] <= 0
+  puts "Invalid K value #{options[:k]}"
+  puts optparse
+  exit
+end
+
+unless File.exist?(options[:file])
+  puts "File #{options[:file]} does not exist"
+  puts options
+  exit
+end
+
+code_to_id, graphs = RCPM.read_file(options[:file])
+cpms_id = {}
+cpms = {}
+
+graphs.each_pair do |year, graph|
+  cpms_id[year] = RCPM.cpm(RCPM.graph_to_matrix(graph), options[:k])
+end
+
+cpms_id.each_pair do |year, cpm|
+  cpms[year] = cpm.map do |nodes|
+    Set.new(nodes.map { |node| code_to_id[year].key(node) })
+  end
+end
+
+cpms.each_pair do |year, cliques|
+  puts "Period: #{year}---------------"
+  cliques.each do |clique|
+    puts clique.to_a.join(",")
+  end
+end

data/bin/setup

@@ -0,0 +1,7 @@
+#!/bin/bash
+set -euo pipefail
+IFS=$'\n\t'
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/ext/bk/bk.c

@@ -0,0 +1,119 @@
+#include <ruby.h>
+
+void print_array(VALUE arr) {
+  printf("%s\n",RSTRING_PTR(rb_inspect(arr)));
+}
+
+void bkv2(VALUE m, VALUE old_set, int ne, int ce, VALUE cliques, VALUE potential_clique) {
+  VALUE new_set;
+
+  int nod, fixp, newne, newce, i, j, count, pos, p, s, sel, minnod;
+
+  new_set = rb_ary_new2(ce);
+  minnod = ce;
+  nod = 0;
+  fixp = 0;
+  pos = 0;
+  s = 0;
+
+  /* Determine each counter value and look for minimum */
+  for (i = 0 ; i < ce && minnod != 0; i++) {
+    p = NUM2INT(rb_ary_entry(old_set, i));
+    count = 0;
+
+    /* Count disconnections */
+    for (j = ne; j < ce && count < minnod; j++) {
+      if(!NUM2INT(rb_ary_entry(rb_ary_entry(m, p), NUM2INT(rb_ary_entry(old_set, j))))) {
+        count++;
+        /* Save position of potential candidate */
+        pos = j;
+      }
+    }
+
+    /* Test new minimum */
+    if (count < minnod) {
+      fixp = p;
+      minnod = count;
+
+      if (i < ne) {
+        s = pos;
+      }
+      else {
+        s = i;
+        /* pre-increment */
+        nod = 1;
+      }
+    }
+  }
+
+  /* If fixed point initially chosen from candidates then
+     number of diconnections will be preincreased by one */
+
+  /* Backtrackcycle */
+  for (nod=minnod+nod; nod>=1; nod--) {
+    /* Interchange */
+    p = NUM2INT(rb_ary_entry(old_set, s));
+    rb_ary_store(old_set, s, rb_ary_entry(old_set, ne));
+    sel = p;
+    rb_ary_store(old_set, ne, INT2NUM(sel));
+
+    /* Fill new set "not" */
+    newne = 0;
+    for (i = 0 ; i < ne ; i++) {
+      if(NUM2INT(rb_ary_entry(rb_ary_entry(m, sel), NUM2INT(rb_ary_entry(old_set, i))))) {
+        rb_ary_store(new_set, newne++, rb_ary_entry(old_set, i));
+      }
+    }
+
+    /*Fill new set "cand" */
+    newce = newne;
+    for (i=ne+1; i < ce; i++) {
+      if(NUM2INT(rb_ary_entry(rb_ary_entry(m, sel), NUM2INT(rb_ary_entry(old_set, i))))) {
+        rb_ary_store(new_set, newce++, rb_ary_entry(old_set, i));
+      }
+    }
+
+    rb_ary_push(potential_clique, INT2NUM(sel));
+
+    if (newce == 0) {
+      rb_ary_push(cliques, rb_ary_dup(potential_clique));
+    }
+    else if (newne < newce) {
+      bkv2(m, new_set, newne, newce, cliques, potential_clique);
+    }
+
+    rb_ary_pop(potential_clique);
+
+    /* Add to "not" */
+    ne++;
+    if (nod > 1) {
+      /* Select a candidate disconnected to the fixed point */
+
+      for(s = ne; NUM2INT((rb_ary_entry(rb_ary_entry(m, fixp), NUM2INT(rb_ary_entry(old_set, s))))); s++);
+    }
+
+  } /* Backtrackcycle */
+}
+
+static VALUE bk(VALUE arr) {
+  int i, n;
+  VALUE all, cliques, potential_clique;
+  
+  n = RARRAY_LEN(arr);
+
+  all = rb_ary_new2(n);
+  potential_clique = rb_ary_new();
+  cliques = rb_ary_new();
+  
+  for (i = 0; i < n; i++) {
+    rb_ary_push(all, INT2NUM(i));
+  }
+
+  bkv2(arr, all, 0, n, cliques, potential_clique);
+
+  return cliques;
+}
+
+void Init_bk() {
+  rb_define_method(rb_cArray, "bk", bk, 0);
+}

data/ext/bk/extconf.rb

@@ -0,0 +1,5 @@
+require "mkmf"
+
+$CFLAGS << ' -O3 -Wextra -Wall -pedantic -std=gnu99'
+
+create_makefile "bk"

data/lib/rcpm.rb

@@ -0,0 +1,119 @@
+require "rcpm/version"
+require 'bk'
+
+module RCPM
+  def self.read_file(filename)
+    current_id = {}
+    code_to_id = {}
+    graphs = {}
+
+    CSV.open(filename, headers: [:id1, :id2, :year]).each do |line|
+      year = line[:year]
+
+      current_id[year] ||= -1
+      code_to_id[year] ||= {}
+      graphs[year] ||= []
+
+      id1 = code_to_id[year][line[:id1]] ||= current_id[year] += 1
+      id2 = code_to_id[year][line[:id2]] ||= current_id[year] += 1
+
+      graphs[year] << [id1,id2]
+    end
+
+    return [code_to_id, graphs]
+  end
+
+  def self.graph_to_matrix(ary)
+    max = ary.flatten.max
+
+    matrix = Array.new(max + 1) { Array.new(max + 1, 0) }
+
+    0.upto(max - 1) { |i| matrix[i][i] = 1 }
+
+    ary.each do |n1, n2|
+      matrix[n1][n2] = 1
+      matrix[n2][n1] = 1
+    end
+
+    return matrix
+  end
+
+  def self.cpm(g, k)
+    cliques_to_components = {}
+    current_component = 0
+
+    cliques = g.bk.select{|cl| cl.size >= k}
+
+    nodes_to_cliques = nodes_to_cliques(cliques)
+
+    #Para cada uma das cliques
+    cliques.each do |clique|
+
+      #Se ela ainda não possui componente(não foi processada)
+      if !cliques_to_components.key?(clique)
+        current_component += 1
+        #Adiciona um novo componente para ela
+        cliques_to_components[clique] = current_component
+        #Coloca esta clique na fronteira
+        frontier = [clique]
+
+        #Enquanto fronteira não for vazia
+        while current_clique = frontier.pop
+          #Pega todas as cliques vizinhas de current_clique
+          get_adjacent_cliques(current_clique, nodes_to_cliques).each do |neighbour|
+            #Se neighbour tem uma interseção com current_clique de tamanho >= k - 1
+            if (current_clique & neighbour).size >= k - 1
+              #Então neighbour também faz parte de current_component
+              cliques_to_components[neighbour] = current_component
+              #Adiciona neighbour à frontier
+              frontier << neighbour
+              #E para cada node de neighbour
+              neighbour.each do |node|
+                #Remove ele da lista de nós não processados
+                nodes_to_cliques[node].delete(neighbour)
+              end
+            end
+          end
+        end
+      end
+    end
+    #Agora basta unir todos os nós que foram rotulados com o mesmo componente
+    component_to_nodes = {}
+    cliques_to_components.each_pair do |clique, component_clique_in|
+      component_to_nodes[component_clique_in] ||= []
+      component_to_nodes[component_clique_in] += clique
+    end
+
+    return component_to_nodes.values
+  end
+
+  private
+
+  #Cria um hash do tipo node -> [cliques que contém node]
+  def self.nodes_to_cliques(cliques)
+    output = Hash.new {|h,k| h[k] = []}
+
+    cliques.each do |clique|
+      clique.each do |node|
+        output[node] << clique
+      end
+    end
+    return output
+  end
+
+  #Dado uma clique, retorna todas as outras adjacentes à ela. Duas cliques são
+  #adjacentes se elas compartilham ao menos um nó
+  def self.get_adjacent_cliques(clique, nodes_to_cliques)
+    adjacent_cliques = []
+
+    clique.each do |node|
+      nodes_to_cliques[node].each do |adj_clique|
+        if clique != adj_clique
+          adjacent_cliques << adj_clique
+        end
+      end
+    end
+    return adjacent_cliques
+  end
+
+end

data/lib/rcpm/version.rb

@@ -0,0 +1,3 @@
+module RCPM
+  VERSION = "0.1.0"
+end

data/rcpm.gemspec

@@ -0,0 +1,24 @@
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'rcpm/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "rcpm"
+  spec.version       = RCPM::VERSION
+  spec.authors       = ["Michel Boaventura"]
+  spec.email         = ["michel.boaventura@gmail.com"]
+
+  spec.summary       = %q{Ruby's implementation of Clique Percolation Method}
+  spec.homepage      = "http://github.com/michelboaventura/rcpm"
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
+  spec.executables   = ["rcpm"]
+  spec.require_paths = ["lib"]
+
+  spec.extensions = %w[ext/bk/extconf.rb]
+
+  spec.add_development_dependency "bundler", "~> 1.8"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "rake-compiler", "~> 0.9"
+end

metadata

@@ -0,0 +1,102 @@
+--- !ruby/object:Gem::Specification
+name: rcpm
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Michel Boaventura
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2015-05-07 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.8'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.8'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: rake-compiler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.9'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.9'
+description: 
+email:
+- michel.boaventura@gmail.com
+executables:
+- rcpm
+extensions:
+- ext/bk/extconf.rb
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- CODE_OF_CONDUCT.md
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/console
+- bin/rcpm
+- bin/setup
+- ext/bk/bk.c
+- ext/bk/extconf.rb
+- lib/rcpm.rb
+- lib/rcpm/version.rb
+- rcpm.gemspec
+homepage: http://github.com/michelboaventura/rcpm
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.4.6
+signing_key: 
+specification_version: 4
+summary: Ruby's implementation of Clique Percolation Method
+test_files: []